Error in combineTCR() with contig_mixcr.csv file

[linderss]

Hi,

thanks Nick for your great package. I wanted to analyse public dataset from Gueguen et al where "filtered_contig_annotations_mixcr.csv" files are available. I haven't had any experience with mixcr before and I'm unsure how to fix the following error.

samples<- c("P47_Tumor_VDJ","P55_Tumor_VDJ","P57_Blood_VDJ", "P57_Tumor_VDJ","P58_Blood_VDJ","P58_Tumor_VDJ","P60_Blood_VDJ","P60_Juxta_VDJ","P60_Tumor_VDJ","P61_Blood_VDJ","P61_Juxta_VDJ","P61_Tumor_VDJ")
file_paths <- paste0("/data/path/", samples,"/outs/filtered_contig_annotations_mixcr.csv")

contig_list <- lapply(file_paths, read.csv)

combined <- combineTCR(contig_list, samples = c("P47_Tumor_VDJ","P55_Tumor_VDJ","P57_Blood_VDJ", "P57_Tumor_VDJ","P58_Blood_VDJ","P58_Tumor_VDJ","P60_Blood_VDJ","P60_Juxta_VDJ","P60_Tumor_VDJ","P61_Blood_VDJ","P61_Juxta_VDJ","P61_Tumor_VDJ"), filterMulti = FALSE, removeMulti = FALSE)

The error i get is the following (which makes sense because my contig list does not have these columns, see screenshot below):

Error in `mutate()`:
ℹ In argument: `TCR1 = ifelse(...)`.
Caused by error:
! object 'v_gene' not found
Backtrace:
  1. scRepertoire::combineTCR(...)
 14. stringr::str_replace_na(v_gene)
 15. stringi::stri_replace_na(string, replacement)

Is there any way to use these contig files with scRepertoire?

[ncborcherding]

Hey @linderss,

Looks like the headers/format for the linked contigs are slightly off than the expected clones.tsv output for MiXCR.

Here is an example of the expected input.

Probably the quickest fix is manually altering the contig_annotation files from the repo you link. Happy to help with this, but it seems to be a bespoke issue with formating of that repo.

Nick

[ncborcherding]

I am going to close this issue due to inactivity.