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Fix bug for no indels #166

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Aug 23, 2023
Merged

Fix bug for no indels #166

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46 changes: 24 additions & 22 deletions R/check_on_ref_genome.R
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Original file line number Diff line number Diff line change
Expand Up @@ -51,26 +51,26 @@ check_on_ref_genome <-function(sumstats_dt,
#if indels in dataset, don't check they are present on the ref
# genome as they won't be there
if(indels){
data.table::setkey(sumstats_dt, SNP)
#make copy, check if not pres in ref first
indel_dt <-
data.table::copy(sumstats_dt[!unique(rsids$SNP),])
#also check >1 character in A1 A2, use this to define indel
indel_dt <- indel_dt[(nchar(A1)>1 | nchar(A2)>1),]
if(nrow(indel_dt)>0){
#remove indels from sumstats for now
sumstats_dt <- sumstats_dt[!indel_dt$SNP, ]
msg <- paste0("Found ",
formatC(nrow(indel_dt),big.mark = ","),
" Indels. These won't",
" be checked against the reference ",
"genome as it does not contain ",
"Indels.\nWARNING If your sumstat ",
"doesn't contain Indels, set the ",
"indel param to FALSE & rerun ",
"MungeSumstats::format_sumstats()")
message(msg)
}
data.table::setkey(sumstats_dt, SNP)
#make copy, check if not pres in ref first
indel_dt <-
data.table::copy(sumstats_dt[!unique(rsids$SNP),])
#also check >1 character in A1 A2, use this to define indel
indel_dt <- indel_dt[(nchar(A1)>1 | nchar(A2)>1),]
if(nrow(indel_dt)>0){
#remove indels from sumstats for now
sumstats_dt <- sumstats_dt[!indel_dt$SNP, ]
msg <- paste0("Found ",
formatC(nrow(indel_dt),big.mark = ","),
" Indels. These won't",
" be checked against the reference ",
"genome as it does not contain ",
"Indels.\nWARNING If your sumstat ",
"doesn't contain Indels, set the ",
"indel param to FALSE & rerun ",
"MungeSumstats::format_sumstats()")
message(msg)
}
}else{
# join using SNP
data.table::setkey(sumstats_dt, SNP)
Expand Down Expand Up @@ -115,8 +115,10 @@ check_on_ref_genome <-function(sumstats_dt,
if (imputation_ind &&
!"IMPUTATION_SNP" %in% names(sumstats_dt)) {
sumstats_dt[, IMPUTATION_SNP := NA]
#update for indels so can rbind later
indel_dt[, IMPUTATION_SNP := NA]
# update for indels so can rbind later
if(indels){
indel_dt[, IMPUTATION_SNP := NA]
}
}
sumstats_dt <-
data.table::rbindlist(
Expand Down
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