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sampleSwaps bugfix #797

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sampleSwaps bugfix #797

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891ce0a
bugfix: samples with no snps ignored
loipf Jan 11, 2022
afd64a4
additional info output about samples with no snps
loipf Jan 11, 2022
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23 changes: 13 additions & 10 deletions R/sample_swap.R
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Original file line number Diff line number Diff line change
Expand Up @@ -86,19 +86,21 @@ sampleSwaps = function(bams = NULL, build = "hg19", prefix = NULL, add = TRUE, m
rc_df = rc_df[complete.cases(rc_df),]

cat("Performing pairwise comparison..\n")
sample_matches = parallel::mclapply(seq_along(rc_af), function(idx){
rc_af_snps_found = rc_af[colnames(rc_df)]
samples_no_snps_found = setdiff(names(rc_af), colnames(rc_df))
sample_matches = parallel::mclapply(seq_along(rc_af_snps_found), function(idx){

x = rc_af[[idx]]
if(idx == length(rc_af)){
x = rc_af_snps_found[[idx]]
if(idx == length(rc_af_snps_found)){
return(NULL)
}else{
rest_samps = seq_along(rc_af)[(idx+1):(length(rc_af))]
rest_samps = seq_along(rc_af_snps_found)[(idx+1):(length(rc_af_snps_found))]
}
#rest_samps = setdiff(seq_along(rc_af), idx)
cat("Comparing", names(rc_af)[idx], "against rest..\n")
#rest_samps = setdiff(seq_along(rc_af_snps_found), idx)
cat("Comparing", names(rc_af_snps_found)[idx], "against rest..\n")

x_compare = lapply(rest_samps,function(rest_idx){
y = rc_af[[rest_idx]]
y = rc_af_snps_found[[rest_idx]]

concordant_snps = lapply(seq_along(1:nrow(y)), function(row_idx){
fisher.test(x = matrix(c(x[row_idx, ref_rc], x[row_idx, alt_rc], y[row_idx, ref_rc], y[row_idx, alt_rc]), nrow = 2, ncol = 2))$p.value
Expand All @@ -108,8 +110,8 @@ sampleSwaps = function(bams = NULL, build = "hg19", prefix = NULL, add = TRUE, m
cor_coef = cor.test(x$vaf, y$vaf)$estimate

data.table::data.table(
X_bam = names(rc_af)[idx],
Y_bam = names(rc_af)[rest_idx],
X_bam = names(rc_af_snps_found)[idx],
Y_bam = names(rc_af_snps_found)[rest_idx],
concordant_snps = concordant_snps[[1]],
discordant_snps = concordant_snps[[2]],
fract_concordant_snps = prop.table(concordant_snps)[[1]],
Expand Down Expand Up @@ -143,6 +145,7 @@ sampleSwaps = function(bams = NULL, build = "hg19", prefix = NULL, add = TRUE, m
fill = TRUE
),
pairwise_comparison = data.table::rbindlist(sample_matches)[order(XY_possibly_paired, decreasing = TRUE)],
BAM_matches = pos_mathces
BAM_matches = pos_mathces,
samples_no_snps_found = samples_no_snps_found
)
}