-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrun_Bay2Ctrls.R
1049 lines (919 loc) · 47.2 KB
/
run_Bay2Ctrls.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
library(spp)
library(Bay2Ctrls)
args <- commandArgs(trailingOnly=TRUE); # Read Arguments from command line
nargs = length(args); # number of arguments
get.file.parts <- function(file.fullpath) {
if (! is.character(file.fullpath)) {
stop('File name must be a string')
}
file.parts <- strsplit(as.character(file.fullpath), .Platform$file.sep, fixed=TRUE)[[1]] # split on file separator
if (length(file.parts) == 0) { # if empty file name
return(list(path='',
fullname='',
name='',
ext='')
)
} else {
if (length(file.parts) == 1) { # if no path then just the file name itself
file.path <- '.'
file.fullname <- file.parts
} else {
file.path <- paste(file.parts[1:(length(file.parts)-1)], collapse=.Platform$file.sep) # 1:last-1 token is path
file.fullname <- file.parts[length(file.parts)] # last token is filename
}
file.fullname.parts <- strsplit(file.fullname,'.',fixed=TRUE)[[1]] # split on .
if (length(file.fullname.parts) == 1) { # if no extension
file.ext <- ''
file.name <- file.fullname.parts
} else {
file.ext <- paste('.', file.fullname.parts[length(file.fullname.parts)], sep="") # add the . to the last token
file.name <- paste(file.fullname.parts[1:(length(file.fullname.parts)-1)], collapse=".")
}
return(list(path=file.path,
fullname=file.fullname,
name=file.name,
ext=file.ext))
}
} # end: get.file.parts()
parse.arguments <- function(args) {
# Set arguments to default values
ip.file <- NA # main ChIP tagAlign/BAM file name
isurl.ip.file <- FALSE # flag indicating whether ChIP file is a URL
input4ip.file <- NA # control tagAlign/BAM file name
isurl.input4ip.file <- FALSE # flag indicating whether control file is a URL
mock.file <- NA
isurl.mock.file <- FALSE
input4mock.file <- NA
isurl.input4mock.file <- FALSE
totReads <- 1e+7
wdfold <- 0
mcstep <- 1e+6
flagShift <- 0
rgn <- "mock"
weightspp <- 1
weightmc <- 1
rmAbnormal <- 1 # 0 no remove, 1 w/ remove
mthd <- 'mcbin'
rankby <- 'spp'
# mcbin parameters: spp, pvaap, pvab, pvmc,
# poisson parameters: signal, pvalue
sep.min <- -100 # min strand shift
sep.max <- 600 # max strand shift
sep.bin <- 5 # increment for strand shift
sep.peak <- NA # user-defined peak shift
exclude.min <- 10 # lowerbound of strand shift exclusion region
exclude.max <- NaN # upperbound of strand shift exclusion region
n.nodes <- NA # number of parallel processing nodes
fdr <- 0.01 # false discovery rate threshold for peak calling
npeak <- NA # threshold on number of peaks to call
temp.dir <- tempdir() # temporary directory
chrname.rm.pattern <- NA # chromosome name pattern used to remove tags
output.odir <- NA # Output directory name
output.npeak.file <- NA # Output narrowPeak file name
output.rpeak.file <- NA # Output regionPeak file name
output.rdata.file <- NA # Rdata file
output.plot.file <- NA # cross correlation plot file
output.result.file <- NA # result file
replace.flag <- FALSE # replace file flag
clean.files.flag <- FALSE # file deletion flag
# Parse arguments
for (each.arg in args) {
if (grepl('^-ip=',each.arg)) { #-c=<chip.file> IP data, a
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
ip.file <- arg.split[2] # second part is chip.file
} else {
stop('No tagAlign/BAM file name provided for parameter -ip=')
}
} else if (grepl('^-input4ip=',each.arg)) { #-i=<control.file>, control of IP, ap
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
input4ip.file <- arg.split[2] # second part is control.file
}
} else if (grepl('^-mock=',each.arg)) { # mock IP data, b
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
mock.file <- arg.split[2] # second part is chip.file
}
} else if (grepl('^-input4mock=',each.arg)) { # control of mock IP
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
input4mock.file <- arg.split[2] # second part is control.file
}
} else if (grepl('^-mcstep=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
mcstep <- as.numeric(arg.split[2]) # second part is chip.file
}
} else if (grepl('^-mthd=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
mthd <- as.character(arg.split[2]) # second part is chip.file
}
} else if (grepl('^-totReads=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
totReads <- as.numeric(arg.split[2]) # second part is chip.file
} else {
totReads <- 1e+7
}
} else if (grepl('^-rankby=',each.arg)) { #-rankby= for poisson "pvalue or ratio"; for
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
rankby <- as.character(arg.split[2]) # second part is chip.file
} else {
rankby <- "spp"
}
} else if (grepl('^-wdfold=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
wdfold <- as.numeric(arg.split[2]) # second part is chip.file
} else {
wdfold <- 0
}
} else if (grepl('^-flagShift=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
flagShift <- as.numeric(arg.split[2]) # second part is chip.file
} else {
flagShift <- 0
}
} else if (grepl('^-rgn=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
rgn <- as.character(arg.split[2]) # second part is chip.file
} else {
rgn <- "mock"
}
} else if (grepl('^-weightmc=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
weightmc <- as.numeric(arg.split[2]) # second part is chip.file
} else {
weightmc <- 1
}
} else if (grepl('^-weightspp=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
weightspp <- as.numeric(arg.split[2]) # second part is chip.file
} else {
weightspp <- 1
}
} else if (grepl('^-rmAbnormal=',each.arg)) { #-c=<chip.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
rmAbnormal <- as.numeric(arg.split[2]) # second part is chip.file
} else {
rmAbnormal <- 1 # 0 do not remove; 1 remove
}
} else if (grepl('^-s=',each.arg)) { #-s=<sep.min>:<sep.bin>:<sep.max>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
sep.vals <- arg.split[2] # second part is sepmin:sepbin:sepmax
sep.vals.split <- strsplit(sep.vals,':',fixed=TRUE)[[1]] # split on :
if (length(sep.vals.split) != 3) { # must have 3 parts
stop('Strand shift limits must be specified as -s=sepmin:sepbin:sepmax')
} else {
if (any(is.na(as.numeric(sep.vals.split)))) { # check that sep vals are numeric
stop('Strand shift limits must be numeric values')
}
sep.min <- round(as.numeric(sep.vals.split[1]))
sep.bin <- round(as.numeric(sep.vals.split[2]))
sep.max <- round(as.numeric(sep.vals.split[3]))
if ((sep.min > sep.max) || (sep.bin > (sep.max - sep.min)) || (sep.bin < 0)) {
stop('Illegal separation values -s=sepmin:sepbin:sepmax')
}
}
} else {
stop('Strand shift limits must be specified as -s=sepmin:sepbin:sepmax')
}
} else if (grepl('^-speak=',each.arg)) { #-speak=<sep.peak> , user-defined cross-correlation peak strandshift
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
sep.peak <- arg.split[2] # second part is <sep.peak>
if (is.na(as.numeric(sep.peak))) { # check that sep.peak is numeric
stop('-speak=<sep.peak>: User defined peak shift must be numeric')
}
sep.peak <- as.numeric(sep.peak)
} else {
stop('User defined peak shift must be provided as -speak=<sep.peak>')
}
} else if (grepl('^-x=',each.arg)) { #-x=<exclude.min>:<exclude.max>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
exclude.vals <- arg.split[2] # second part is excludemin:excludemax
exclude.vals.split <- strsplit(exclude.vals,':',fixed=TRUE)[[1]] # split on :
if (length(exclude.vals.split) != 2) { # must have 2 parts
stop('Exclusion limits must be specified as -x=excludemin:excludemax')
} else {
if (any(is.na(as.numeric(exclude.vals.split)))) { # check that exclude vals are numeric
stop('Exclusion limits must be numeric values')
}
exclude.min <- round(as.numeric(exclude.vals.split[1]))
exclude.max <- round(as.numeric(exclude.vals.split[2]))
if (exclude.min > exclude.max) {
stop('Illegal exclusion limits -x=excludemin:excludemax')
}
}
} else {
stop('Exclusion limits must be specified as -x=excludemin:excludemax')
}
} else if (grepl('^-p=',each.arg)) { #-p=<n.nodes> , number of parallel processing nodes, default=NULL
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
n.nodes <- arg.split[2] # second part is numnodes
if (is.na(as.numeric(n.nodes))) { # check that n.nodes is numeric
stop('-p=<numnodes>: numnodes must be numeric')
}
n.nodes <- round(as.numeric(n.nodes))
} else {
stop('Number of parallel nodes must be provided as -p=<numnodes>')
}
} else if (grepl('^-fdr=',each.arg)) { #-fdr=<fdr> , false discovery rate, default=0.01
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
fdr <- arg.split[2] # second part is fdr
if (is.na(as.numeric(fdr))) { # check that fdr is numeric
stop('-fdr=<falseDiscoveryRate>: false discovery rate must be numeric')
}
fdr <- as.numeric(fdr)
} else {
stop('False discovery rate must be provided as -fdr=<fdr>')
}
} else if (grepl('^-npeak=',each.arg)) { #-npeak=<numPeaks> , number of peaks threshold, default=NA
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
npeak <- arg.split[2] # second part is npeak
if (is.na(as.numeric(npeak))) { # check that npeak is numeric
stop('-npeak=<numPeaks>: threshold on number of peaks must be numeric')
}
npeak <- round(as.numeric(npeak))
} else {
stop('Threshold on number of peaks must be provided as -npeak=<numPeaks>')
}
} else if (grepl('^-tmpdir=',each.arg)) { #-tmpdir=<temp.dir>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
temp.dir <- arg.split[2] # second part is temp.dir
} else {
stop('No temporary directory provided for parameter -tmpdir=')
}
} else if (grepl('^-filtchr=',each.arg)) { #-filtchr=<chrname.rm.pattern>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
chrname.rm.pattern <- arg.split[2] # second part is chrname.rm.pattern
} else {
stop('No pattern provided for parameter -filtchr=')
}
} else if (grepl('^-odir=',each.arg)) { #-odir=<output.odir>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
output.odir <- arg.split[2] # second part is output.odir
} else {
stop('No output directory provided for parameter -odir=')
}
} else if (grepl('^-savn',each.arg)) { # -savn=<output.npeak.file> OR -savn , save narrowpeak
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2])) {
output.npeak.file <- arg.split[2] #-savn=
} else if (each.arg=='-savn') {
output.npeak.file <- NULL # NULL indicates get the name from the main file name
} else {
stop('Argument for saving narrowPeak file must be -savn or -savn=<filename>')
}
} else if (grepl('^-savr',each.arg)) { # -savr=<output.rpeak.file> OR -savr , save regionpeak
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2])) {
output.rpeak.file <- arg.split[2] #-savr=
} else if (each.arg=='-savr') {
output.rpeak.file <- NULL # NULL indicates get the name from the main file name
} else {
stop('Argument for saving regionPeak file must be -savr or -savr=<filename>')
}
} else if (grepl('^-savd',each.arg)) { # -savd=<output.rdata.file> OR -savd , save Rdata file
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2])) {
output.rdata.file <- arg.split[2] #-savd=
} else if (each.arg=='-savd') {
output.rdata.file <- NULL # NULL indicates get the name from the main file name
} else {
stop('Argument for saving Rdata file must be -savd or -savd=<filename>')
}
} else if (grepl('^-savp',each.arg)) { # -savp=<output.plot.file> OR -savp , save cross-correlation plot
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2])) {
output.plot.file <- arg.split[2] #-savp=
} else if (each.arg=='-savp') {
output.plot.file <- NULL # NULL indicates get the name from the main file name
} else {
stop('Argument for saving Rdata file must be -savp or -savp=<filename>')
}
} else if (grepl('^-out=',each.arg)) { #-out=<output.result.file>
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
if (! is.na(arg.split[2]) ) {
output.result.file <- arg.split[2] # second part is output.result.file
} else {
stop('No result file provided for parameter -out=')
}
} else if (each.arg == '-rf') {
replace.flag <- TRUE
} else if (each.arg == '-clean') {
clean.files.flag <- TRUE
} else {
stop('Illegal argument ',each.arg)
}
}
# End: for loop
# Check arg combination
if (wdfold != 0 & flagShift == 0) {
stop('wdfold anc flagShift problem')
}
# Check mandatory arguments
if (is.na(ip.file)) {
stop('-ip=<tagAlign/BAMFileName> is a mandatory argument')
}
# Correct other arguments
if (is.na(output.odir)) { # Reconstruct output.odir if not provided
output.odir <- get.file.parts(ip.file)$path
}
chip.file <- ip.file
if (! is.na(mock.file)) {
control.file <- mock.file
}else if(! is.na(input4ip.file)) {
control.file <- input4ip.file
}
if (is.null(output.npeak.file)) { # Reconstruct output.npeak.file if NULL
output.npeak.file <- file.path(output.odir, paste(get.file.parts(chip.file)$name, '_VS_', get.file.parts(control.file)$name,'.narrowPeak', sep=""))
}
if (is.null(output.rpeak.file)) { # Reconstruct output.rpeak.file if NULL
output.rpeak.file <- file.path(output.odir, paste(get.file.parts(chip.file)$name, '_VS_', get.file.parts(control.file)$name,'.regionPeak', sep=""))
}
if (is.null(output.rdata.file)) { # Reconstruct output.rdata.file if NULL
output.rdata.file <- file.path(output.odir, paste(get.file.parts(chip.file)$name, '.Rdata', sep=""))
}
if (is.null(output.plot.file)) { # Reconstruct output.plot.file if NULL
output.plot.file <- file.path(output.odir, paste(get.file.parts(chip.file)$name, '.pdf', sep=""))
}
return(list(ip.file=ip.file,
input4ip.file=input4ip.file,
mock.file=mock.file,
input4mock.file=input4mock.file,
totReads=totReads,
wdfold=wdfold,
mcstep=mcstep,
flagShift=flagShift,
rgn=rgn,
rankby=rankby,
weightspp=weightspp,
weightmc=weightmc,
rmAbnormal=rmAbnormal,
mthd=mthd,
sep.range=c(sep.min,sep.bin,sep.max),
sep.peak=sep.peak,
ex.range=c(exclude.min,exclude.max),
n.nodes=n.nodes,
fdr=fdr,
npeak=npeak,
temp.dir=temp.dir,
chrname.rm.pattern=chrname.rm.pattern,
output.odir=output.odir,
output.npeak.file=output.npeak.file,
output.rpeak.file=output.rpeak.file,
output.rdata.file=output.rdata.file,
output.plot.file=output.plot.file,
output.result.file=output.result.file,
replace.flag=replace.flag,
clean.files.flag=clean.files.flag))
} # end: parse.arguments()
read.align <- function(align.filename) {
# ===================================
# Function will read a tagAlign or BAM file
# ===================================
if (grepl('(\\.bam)?.*(\\.tagAlign)',align.filename)) { # if tagalign file
chip.data <- read.tagalign.tags(align.filename)
# get readlength info
tmpDataRows <- read.table(align.filename,nrows=500)
chip.data$read.length <- round(median(tmpDataRows$V3 - tmpDataRows$V2))
} else if (grepl('(\\.tagAlign)?.*(\\.bam)',align.filename)) { # if bam file
# create BAM file name
bam2align.filename <- sub('\\.bam','.tagAlign',align.filename)
# generate command to convert bam to tagalign
command <- vector(length=2)
command[1] <- sprintf("samtools view -F 0x0204 -o - %s",align.filename)
command[2] <- paste("awk 'BEGIN{FS=" , '"\t"' , ";OFS=", '"\t"} {if ($2==16) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"}}', "' 1> ", bam2align.filename, sep="")
# command[2] <- paste("awk 'BEGIN{OFS=", '"\t"} {if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"}}', "' 1> ", bam2align.filename, sep="")
command <- paste(command,collapse=" | ")
cat(command,"\n")
# Run command
status <- system(command,intern=FALSE,ignore.stderr=FALSE)
if ((status != 0) || !file.exists(bam2align.filename)) {
cat(sprintf("Error converting BAM to tagalign file: %s\n",align.filename),file=stderr())
q(save="no",status=1)
}
# read converted BAM file
chip.data <- read.tagalign.tags(bam2align.filename)
# get readlength info
tmpDataRows <- read.table(bam2align.filename,nrows=500)
chip.data$read.length <- round(median(tmpDataRows$V3 - tmpDataRows$V2))
# delete temporary tagalign file
file.remove(bam2align.filename)
} else {
cat(sprintf("Error:Unknown file format for file:%s\n",align.fname),file=stderr())
q(save="no",status=1)
}
return(chip.data)
} # end: read.align()
print.run.params <- function(iparams){
# ===================================
# Output run parameters
# ===================================
cat('################\n',file=stdout())
cat(iparams$ip.file,
iparams$input4ip.file,
iparams$sep.range,
iparams$sep.peak,
iparams$ex.range,
iparams$n.nodes,
iparams$fdr,
iparams$npeak,
iparams$output.odir,
iparams$output.npeak.file,
iparams$output.rpeak.file,
iparams$output.rdata.file,
iparams$output.plot.file,
iparams$output.result.file,
iparams$replace.flag,
labels=c(
'ChIP data:',
'Control data:',
'strandshift(min):',
'strandshift(step):',
'strandshift(max)',
'user-defined peak shift',
'exclusion(min):',
'exclusion(max):',
'num parallel nodes:',
'FDR threshold:',
'NumPeaks Threshold:',
'Output Directory:',
'narrowPeak output file name:',
'regionPeak output file name:',
'Rdata filename:',
'plot pdf filename:',
'result filename:',
'Overwrite files?:'),
fill=18,
file=stdout())
cat('\n',file=stdout())
} # end: print.run.parameters()
check.replace.flag <- function(iparams){
# ===================================
# Check if files exist
# ===================================
# If replace.flag is NOT set, check if output files exist and abort if necessary
if (! iparams$replace.flag) {
if (! is.na(iparams$output.npeak.file)) {
if (file.exists(iparams$output.npeak.file)) {
cat('narrowPeak file already exists. Aborting Run. Use -rf if you want to overwrite\n',file=stderr())
q(save="no",status=1)
}
}
if (! is.na(iparams$output.rpeak.file)) {
if (file.exists(iparams$output.rpeak.file)) {
cat('regionPeak file already exists. Aborting Run. Use -rf if you want to overwrite\n',file=stderr())
q(save="no",status=1)
}
}
if (! is.na(iparams$output.plot.file)) {
if (file.exists(iparams$output.plot.file)) {
cat('Plot file already exists. Aborting Run. Use -rf if you want to overwrite\n',file=stderr())
q(save="no",status=1)
}
}
if (! is.na(iparams$output.rdata.file)) {
if (file.exists(iparams$output.rdata.file)) {
cat('Rdata file already exists. Aborting Run. Use -rf if you want to overwrite\n',file=stderr())
q(save="no",status=1)
}
}
}
}
# #############################################################################
# MAIN FUNCTION
# #############################################################################
#print("here2\n");
# Check number of arguments
minargs = 1;
maxargs = 40;
iparams <- parse.arguments(args)
# Print run parameters
print.run.params(iparams)
# Check if output files exist
#check.replace.flag(iparams)
# curr.chip.file and curr.control.file always point to the original ChIP and control files on disk
# ta.chip.filename & ta.control.filename always point to the final but temporary versions of the ChIP and control files that will be passed to read.align
# Download ChIP and control files if necessary to temp.dir
curr.ip.file <- iparams$ip.file
curr.input4ip.file <- iparams$input4ip.file
curr.mock.file <- iparams$mock.file
curr.input4mock.file <- iparams$input4mock.file
# unzip ChIP and input files if required AND copy to temp directory
if (get.file.parts(curr.ip.file)$ext == '.gz') {
ta.ip.filename <- tempfile(get.file.parts(curr.ip.file)$name, tmpdir=iparams$temp.dir) # unzip file to temp.dir/[filename with .gz removed][randsuffix]
cat('Decompressing ChIP file\n',file=stdout())
if (system(paste("gunzip -c",curr.ip.file,">",ta.ip.filename)) != 0) {
stop('Unable to decompress file:', iparams$ip.file)
}
if (iparams$clean.files.flag) { # Remove original file if clean.files.flag is set
file.remove(curr.ip.file)
}
} else {
ta.ip.filename <- tempfile(get.file.parts(curr.ip.file)$fullname, tmpdir=iparams$temp.dir)
if (iparams$clean.files.flag) {
file.rename(curr.ip.file,ta.ip.filename) # move file to temp.dir/[filename][randsuffix]
} else {
file.copy(curr.ip.file,ta.ip.filename) # copy file to temp.dir/[filename][randsuffix]
}
}
if (! is.na(iparams$mock.file)) {
if (get.file.parts(curr.mock.file)$ext == '.gz') {
ta.mock.filename <- tempfile(get.file.parts(curr.mock.file)$name, tmpdir=iparams$temp.dir) # unzip file to temp.dir/[filename with .gz removed][randsuffix]
cat('Decompressing mockIP file\n',file=stdout())
if (system(paste("gunzip -c",curr.mock.file,">",ta.mock.filename)) != 0) {
stop('Unable to decompress file:', iparams$mock.file)
}
if (iparams$clean.files.flag) { # Remove original file if clean.files.flag is set
file.remove(curr.mock.file)
}
} else {
ta.mock.filename <- tempfile(get.file.parts(curr.mock.file)$fullname, tmpdir=iparams$temp.dir)
if (iparams$clean.files.flag) {
file.rename(curr.mock.file,ta.mock.filename) # move file to temp.dir/[filename][randsuffix]
} else {
file.copy(curr.mock.file,ta.mock.filename) # copy file to temp.dir/[filename][randsuffix]
}
}
}
if (! is.na(iparams$input4ip.file)) {
if (get.file.parts(curr.input4ip.file)$ext == '.gz') {
ta.input4ip.filename <- tempfile(get.file.parts(curr.input4ip.file)$name, tmpdir=iparams$temp.dir) # unzip file to temp.dir/[filename with .gz removed][randsuffix]
cat('Decompressing control file\n',file=stdout())
if (system(paste("gunzip -c",curr.input4ip.file,">",ta.input4ip.filename)) != 0) {
stop('Unable to decompress file:', iparams$input4ip.file)
}
if (iparams$clean.files.flag) { # Remove original file if clean.files.flag is set
file.remove(curr.input4ip.file)
}
} else {
ta.input4ip.filename <- tempfile(get.file.parts(curr.input4ip.file)$fullname, tmpdir=iparams$temp.dir) # copy file to temp.dir/[filename][randsuffix]
if (iparams$clean.files.flag) {
file.rename(curr.input4ip.file,ta.input4ip.filename) # move file to temp.dir/[filename][randsuffix]
} else {
file.copy(curr.input4ip.file,ta.input4ip.filename) # copy file to temp.dir/[filename][randsuffix]
}
}
}
if (! is.na(iparams$input4mock.file)) {
if (get.file.parts(curr.input4mock.file)$ext == '.gz') {
ta.input4mock.filename <- tempfile(get.file.parts(curr.input4mock.file)$name, tmpdir=iparams$temp.dir) # unzip file to temp.dir/[filename with .gz removed][randsuffix]
cat('Decompressing controlMockIP file\n',file=stdout())
if (system(paste("gunzip -c",curr.input4mock.file,">",ta.input4mock.filename)) != 0) {
stop('Unable to decompress file:', iparams$input4mock.file)
}
if (iparams$clean.files.flag) { # Remove original file if clean.files.flag is set
file.remove(curr.input4mock.file)
}
} else {
ta.input4mock.filename <- tempfile(get.file.parts(curr.input4mock.file)$fullname, tmpdir=iparams$temp.dir) # copy file to temp.dir/[filename][randsuffix]
if (iparams$clean.files.flag) {
file.rename(curr.input4mock.file,ta.input4mock.filename) # move file to temp.dir/[filename][randsuffix]
} else {
file.copy(curr.input4mock.file,ta.input4mock.filename) # copy file to temp.dir/[filename][randsuffix]
}
}
}
# Read ChIP tagAlign/BAM files
#cat("Reading ChIP tagAlign/BAM file",iparams$ip.file,"\n",file=stdout())
ip.data <- read.align(ta.ip.filename)
#cat("ChIP data read length",chip.data$read.length,"\n",file=stdout())
#cat("ChIP data read length",ip.data$read.length,"\n",file=stdout())
file.remove(ta.ip.filename) # Delete temporary file
if (length(ip.data$tags)==0) {
stop('Error in ChIP file format:', iparams$ip.file)
}
# Remove illegal chromosome names
if (! is.na(iparams$chrname.rm.pattern)) {
selectidx <- which(grepl(iparams$chrname.rm.pattern,names(ip.data$tags))==FALSE)
ip.data$tags <- ip.data$tags[selectidx]
ip.data$quality <- ip.data$quality[selectidx]
}
ip.data$num.tags <- sum(unlist(lapply(ip.data$tags,function(d) length(d))))
# Read Control tagAlign/BAM files
if (! is.na(iparams$input4ip.file)) {
cat("Reading Control tagAlign/BAM file",iparams$input4ip.file,"\n",file=stdout())
input4ip.data <- read.align(ta.input4ip.filename)
file.remove(ta.input4ip.filename) # Delete temporary file
if (length(input4ip.data$tags)==0) {
stop('Error in control file format:', iparams$input4ip.file)
}
cat("Control data read length",input4ip.data$read.length,"\n",file=stdout())
# Remove illegal chromosome names
if (! is.na(iparams$chrname.rm.pattern)) {
selectidx <- which(grepl(iparams$chrname.rm.pattern,names(input4ip.data$tags))==FALSE)
input4ip.data$tags <- input4ip.data$tags[selectidx]
input4ip.data$quality <- input4ip.data$quality[selectidx]
}
input4ip.data$num.tags <- sum(unlist(lapply(input4ip.data$tags,function(d) length(d))))
}
if (! is.na(iparams$mock.file)) {
cat("Reading Control tagAlign/BAM file",iparams$mock.file,"\n",file=stdout())
mock.data <- read.align(ta.mock.filename)
file.remove(ta.mock.filename) # Delete temporary file
if (length(mock.data$tags)==0) {
stop('Error in control file format:', iparams$mock.file)
}
cat("mockIP data read length",mock.data$read.length,"\n",file=stdout())
# Remove illegal chromosome names
if (! is.na(iparams$chrname.rm.pattern)) {
selectidx <- which(grepl(iparams$chrname.rm.pattern,names(mock.data$tags))==FALSE)
mock.data$tags <- mock.data$tags[selectidx]
mock.data$quality <- mock.data$quality[selectidx]
}
mock.data$num.tags <- sum(unlist(lapply(mock.data$tags,function(d) length(d))))
}
if (! is.na(iparams$input4mock.file)) {
cat("Reading Control tagAlign/BAM file",iparams$input4mock.file,"\n",file=stdout())
input4mock.data <- read.align(ta.input4mock.filename)
file.remove(ta.input4mock.filename) # Delete temporary file
if (length(input4mock.data$tags)==0) {
stop('Error in control file format:', iparams$input4mock.file)
}
cat("Control of mockIP data read length",input4mock.data$read.length,"\n",file=stdout())
# Remove illegal chromosome names
if (! is.na(iparams$chrname.rm.pattern)) {
selectidx <- which(grepl(iparams$chrname.rm.pattern,names(input4mock.data$tags))==FALSE)
input4mock.data$tags <- input4mock.data$tags[selectidx]
input4mock.data$quality <- input4mock.data$quality[selectidx]
}
input4mock.data$num.tags <- sum(unlist(lapply(input4mock.data$tags,function(d) length(d))))
}
# Open multiple processes if required
if (is.na(iparams$n.nodes) || iparams$n.nodes == 1) {
cluster.nodes <- NULL
} else {
cat("loading snow\n")
library(snow)
cat("loaded snow\n")
cluster.nodes <- makeCluster(iparams$n.nodes,type="SOCK")
cat("multiple nodes ",cluster.nodes$rank,"\n")
}
# #################################
# Calculate cross-correlation for various strand shifts
# #################################
cat("Calculating peak characteristics\n",file=stdout())
# crosscorr
# $cross.correlation : Cross-correlation profile as an $x/$y data.frame
# $peak : Position ($x) and height ($y) of automatically detected cross-correlation peak.
# $whs: Optimized window half-size for binding detection (based on the width of the cross-correlation peak)
crosscorr <- get.binding.characteristics(ip.data,
srange=iparams$sep.range[c(1,3)],
bin=iparams$sep.range[2],
accept.all.tags=T,
cluster=cluster.nodes)
if (!is.na(iparams$n.nodes) && iparams$n.nodes != 1) {
stopCluster(cluster.nodes)
}
# Smooth the cross-correlation curve if required
cc <- crosscorr$cross.correlation
crosscorr$min.cc <- crosscorr$cross.correlation[ which.min(crosscorr$cross.correlation$y) , ] # minimum value and shift of cross-correlation
cat("Minimum cross-correlation value", crosscorr$min.cc$y,"\n",file=stdout())
cat("Minimum cross-correlation shift", crosscorr$min.cc$x,"\n",file=stdout())
sbw <- 2*floor(ceiling(5/iparams$sep.range[2]) / 2) + 1 # smoothing bandwidth
cc$y <- caTools::runmean(cc$y,sbw,alg="fast")
# Compute cross-correlation peak
bw <- ceiling(2/iparams$sep.range[2]) # crosscorr[i] is compared to crosscorr[i+/-bw] to find peaks
peakidx <- (diff(cc$y,bw)>=0) # cc[i] > cc[i-bw]
peakidx <- diff(peakidx,bw)
peakidx <- which(peakidx==-1) + bw
# exclude peaks from the excluded region
if ( is.nan(iparams$ex.range[2]) ) {
iparams$ex.range[2] <- chip.data$read.length+10
}
peakidx <- peakidx[(cc$x[peakidx] < iparams$ex.range[1]) | (cc$x[peakidx] > iparams$ex.range[2])]
cc <- cc[peakidx,]
# Find max peak position and other peaks within 0.9*max_peakvalue that are further away from maxpeakposition
maxpeakidx <- which.max(cc$y)
maxpeakshift <- cc$x[maxpeakidx]
maxpeakval <- cc$y[maxpeakidx]
peakidx <-which((cc$y >= 0.9*maxpeakval) & (cc$x >= maxpeakshift))
cc <- cc[peakidx,]
# sort the peaks and get the top 3
sortidx <- order(cc$y,decreasing=TRUE)
sortidx <- sortidx[c(1:min(3,length(sortidx)))]
cc.peak <- cc[sortidx,]
# Override peak shift if user supplies peak shift
if (! is.na(iparams$sep.peak)) {
cc.peak <- approx(crosscorr$cross.correlation$x,crosscorr$cross.correlation$y,iparams$sep.peak,rule=2)
}
cat("Peak cross-correlation value", paste(cc.peak$y,collapse=","),"\n",file=stdout())
cat("Peak strand shift",paste(cc.peak$x,collapse=","),"\n",file=stdout())
# Reset values in crosscorr
crosscorr$peak$x <- cc.peak$x[1]
crosscorr$peak$y <- cc.peak$y[1]
# Compute window half size
whs.thresh <- crosscorr$min.cc$y + (crosscorr$peak$y - crosscorr$min.cc$y)/3
crosscorr$whs <- max(crosscorr$cross.correlation$x[crosscorr$cross.correlation$y >= whs.thresh])
cat("Window half size",crosscorr$whs,"\n",file=stdout())
# Compute phantom peak coefficient
ph.peakidx <- which( ( crosscorr$cross.correlation$x >= ( ip.data$read.length - round(2*iparams$sep.range[2]) ) ) &
( crosscorr$cross.correlation$x <= ( ip.data$read.length + round(1.5*iparams$sep.range[2]) ) ) )
ph.peakidx <- ph.peakidx[ which.max(crosscorr$cross.correlation$y[ph.peakidx]) ]
crosscorr$phantom.cc <- crosscorr$cross.correlation[ph.peakidx,]
cat("Phantom peak location",crosscorr$phantom.cc$x,"\n",file=stdout())
cat("Phantom peak Correlation",crosscorr$phantom.cc$y,"\n",file=stdout())
crosscorr$phantom.coeff <- crosscorr$peak$y / crosscorr$phantom.cc$y
crosscorr$phantom.coeff <- crosscorr$peak$y / crosscorr$min.cc$y
cat("Normalized cross-correlation coefficient (NCCC)",crosscorr$phantom.coeff,"\n",file=stdout())
crosscorr$rel.phantom.coeff <- (crosscorr$peak$y - crosscorr$min.cc$y) / (crosscorr$phantom.cc$y - crosscorr$min.cc$y)
cat("Relative Cross correlation Coefficient (RCCC)",crosscorr$rel.phantom.coeff,"\n",file=stdout())
crosscorr$phantom.quality.tag <- NA
if ( (crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < 0.25) ) {
crosscorr$phantom.quality.tag <- -2
} else if ( (crosscorr$rel.phantom.coeff >= 0.25) & (crosscorr$rel.phantom.coeff < 0.5) ) {
crosscorr$phantom.quality.tag <- -1
} else if ( (crosscorr$rel.phantom.coeff >= 0.5) & (crosscorr$rel.phantom.coeff < 1) ) {
crosscorr$phantom.quality.tag <- 0
} else if ( (crosscorr$rel.phantom.coeff >= 1) & (crosscorr$rel.phantom.coeff < 1.5) ) {
crosscorr$phantom.quality.tag <- 1
} else if ( (crosscorr$rel.phantom.coeff >= 1.5) ) {
crosscorr$phantom.quality.tag <- 2
}
cat("Phantom Peak Quality Tag",crosscorr$phantom.quality.tag,"\n",file=stdout())
# Output result to result file if required
#Filename\tnumReads\tPeak_shift\tPeak_Correlation\tRead_length\tPhantomPeak_Correlation\tMin_Correlation_Shift\tMin_Correlation\tNormalized_CrossCorrelation_Coefficient\tRelative_CrossCorrelation_Coefficient\tQualityTag)
if (! is.na(iparams$output.result.file)) {
cat(get.file.parts(iparams$ip.file)$fullname,
ip.data$num.tags,
paste(cc.peak$x,collapse=","),
paste(cc.peak$y,collapse=","),
crosscorr$phantom.cc$x,
crosscorr$phantom.cc$y,
crosscorr$min.cc$x,
crosscorr$min.cc$y,
crosscorr$phantom.coeff,
crosscorr$rel.phantom.coeff,
crosscorr$phantom.quality.tag,
sep="\t",
file=iparams$output.result.file,
append=TRUE)
cat("\n",
file=iparams$output.result.file,
append=TRUE)
}
# Save figure if required
if (! is.na(iparams$output.plot.file)) {
pdf(file=iparams$output.plot.file,width=5,height=5)
par(mar = c(4,3.5,2,0.5), mgp = c(1.5,0.5,0), cex = 0.8);
plot(crosscorr$cross.correlation,
type='l',
xlab=sprintf("strand-shift (%s)",paste(cc.peak$x,collapse=",")),
ylab="cross-correlation")
abline(v=cc.peak$x,lty=2,col=2)
abline(v=crosscorr$phantom.cc$x,lty=2,col=4)
title(main=get.file.parts(iparams$ip.file)$fullname,
sub=sprintf("NSC=%g,RSC=%g,Qtag=%d",crosscorr$phantom.coeff,crosscorr$rel.phantom.coeff,crosscorr$phantom.quality.tag))
dev.off();
}
# Save RData file if required
if (! is.na(iparams$output.rdata.file)) {
save(iparams,
crosscorr,
cc.peak,
file=iparams$output.rdata.file);
}
# #################################
# Call peaks
# #################################
if ( !is.na(iparams$output.npeak.file) || !is.na(iparams$output.rpeak.file) ) {
# Remove local tag anomalies
if(iparams$rmAbnormal == 1){
cat('Removing read stacks\n',file=stdout())
ip.data <- remove.local.tag.anomalies(ip.data$tags)
if (! is.na(iparams$input4ip.file)) {
input4ip.data <- remove.local.tag.anomalies(input4ip.data$tags)
}
if (! is.na(iparams$mock.file)) {
mock.data <- remove.local.tag.anomalies(mock.data$tags)
}
if (! is.na(iparams$input4mock.file)) {
input4mock.data <- remove.local.tag.anomalies(input4mock.data$tags)
}
}
if(iparams$flagShift == 0){
tagShift <- 0
}else{
tagShift <- as.numeric(round(crosscorr$peak$x/2))
tagShift <- mean(tagShift)
}
# Open multiple processes if required
if (is.na(iparams$n.nodes) || iparams$n.nodes == 1) {
cluster.nodes <- NULL
} else {
cluster.nodes <- makeCluster(iparams$n.nodes,type="SOCK")
}
# Find peaks
cat('Finding peaks\n',file=stdout())
if (!is.na(iparams$npeak)) {
iparams$fdr <- 0.99999
}
if(iparams$mthd == 'mcbin'){
if(is.na(iparams$input4mock.file) | is.na(iparams$input4ip.file) | is.na(iparams$mock.file) | is.na(iparams$ip.file) ){
stop ("missing chip-seq data files for mcbin\n")
}
data.a <- ip.data
data.b <- mock.data
data.ap <- input4ip.data
data.bp <- input4mock.data
if(iparams$rgn == "mock"){
narrow.peaks <- find.binding.positions(signal.data=data.a,control.data=data.b,fdr=iparams$fdr,method=tag.lwcc,whs=crosscorr$whs,cluster=cluster.nodes,tec.filter=T,enrichment.z=0,min.thr=0,background.density.scaling = T,min.mle.threshold=0,e.value= 1000000000,enrichment.background.scales=c(1))
}else if( iparams$rgn == "input"){
narrow.peaks <- find.binding.positions(signal.data=data.a,control.data=data.ap,fdr=iparams$fdr,method=tag.lwcc,whs=crosscorr$whs,cluster=cluster.nodes,tec.filter=T,enrichment.z=0,min.thr=0,background.density.scaling = T,min.mle.threshold=0,e.value =1000000000,enrichment.background.scales=c(1))
}else{
stop("-rgn= parameter is missing mock or input?")
}
if (!is.na(iparams$n.nodes) && iparams$n.nodes != 1) {
stopCluster(cluster.nodes)
}
cat(paste("Detected",sum(unlist(lapply(narrow.peaks$npl,function(d) length(d$x)))),"peaks"),"\n",file=stdout())
narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, pv = NA); narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.diff = NA)
narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.a = NA); narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.ap = NA)
narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.bp = NA); narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.b = NA)
narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.ratio = NA); narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, nt.diffRatio = NA)
narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, pvab = NA); narrow.peaks$npl <- lapply(narrow.peaks$npl, cbind, pvaap = NA);
# Compute and write regionPeak file
if (!is.na(iparams$output.rpeak.file)) {
if(iparams$rgn == "mock"){
region.peaks <- add.broad.peak.regions(data.a,data.b,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
}else{
region.peaks <- add.broad.peak.regions(data.a,data.ap,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
}
region.peaks$npl <- add.rsre(region.peaks,margin=round(crosscorr$whs/2))
region.peaks$npl <- add.count4(region.peaks,data.a,data.b,data.ap,data.bp,iparams$totReads,tagShift,iparams$wdfold)
region.peaks$npl <- add.pois(region.peaks,"both")
write.narrowpeak.mcbin(region.peaks,iparams$output.rpeak.file,rby=iparams$rankby,mcstep = iparams$mcstep,coe.mc = iparams$weightmc, coe.spp = iparams$weightspp,npeaks=iparams$npeak)
system(paste('gzip -f ',iparams$output.rpeak.file))
}
}else if(iparams$mthd == 'poisson'){
data.a <- ip.data
if(! is.na(iparams$input4ip.file) & is.na(iparams$mock.file)){
data.ap <- input4ip.data
}else if(is.na(iparams$input4ip.file) & ! is.na(iparams$mock.file)){
data.ap <- mock.data
}else{
stop('chip-seq data file prolem')
}
narrow.peaks <- find.binding.positions(signal.data=data.a,control.data=data.ap,fdr=iparams$fdr,method=tag.lwcc,whs=crosscorr$whs,cluster=cluster.nodes,tec.filter=T,enrichment.z=0,min.thr=0,background.density.scaling = T,min.mle.threshold=0,e.value=1000000000,enrichment.background.scales=c(1))
if (!is.na(iparams$n.nodes) && iparams$n.nodes != 1) {
stopCluster(cluster.nodes)
}