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Questions about compare_junctions_hist_v2.R #178
Description
Thank you for making this super useful software.
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When running "compare_junctions_hist_v2.R", there were multiple NA values in "mean_norm_score_variant". I traced it back to the function starting on line 204, where the unlist (strsplit) functions are needed for the first condition too (added below).
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The example workflow recommends using --variant-grouping=exclude when running stats_wrapper.py. Is there an equivalent feature in "compare_junctions_hist_v2.R"?
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There are duplicates (records with same variant_junction_info) in the final dataset after running "compare_junctions_hist_v2.R". Do you recommend de-duplicating them? If so, how?
a <- function(x, y){
# if(y == "TCGA-ZH-A8Y2-01A,TCGA-ZH-A8Y5-01A"){
# browser()
# }
toAdd <- (str_count(y, ',') + 1) - (str_count(x, ',') + 1)
# browser()
if (toAdd > 0) {
toAdd <- rep(0.0000000, toAdd)
x <- c(unlist(strsplit(x, ",")), toAdd) # added unlist(strsplit) here too
} else {
x <- unlist(strsplit(x, ","))
}
x <- list(x)
return(x)
}
Activity
mguaita commentedon Sep 13, 2024
Hello,
I am still encountering this same issues and others already reported in the compare_junctions of the example WF #153.
@R-Najjar have you been able to gain any insights on your questions?
I have also tried the python version compare_jucntions_hist.py and got a different errors when merging the score data of the samples_with_variants and the samples_wout_variants.
R-Najjar commentedon Sep 14, 2024
@mguaita I gave up on this tool because of these issues.
mguaita commentedon Sep 16, 2024
@R-Najjar thank you for replying.
Have you been able to find any alternative approaches to perform the statistical analysis of the Regtools' output comparisons?