Closed bschilder closed 3 years ago
Fixed by adding the following to check_chr()
#### Remove chr prefix uppercase ####
if(rmv_chrPrefix){
message("Removing 'chr' prefix from CHR.")
sumstats_dt[,CHR:=gsub("chr","",CHR,ignore.case = TRUE)]
}
Users can turn this off with the new rmv_chrPrefix
argument in format_sumstats
Also ensuring that input to rmv_chr
is recognized regardless of the format users provide it in.
rmv_chr=c("X","Y","MT")
### Standardise chromosomes specified
rmv_chr <- toupper(gsub("chr","",rmv_chr,ignore.case = TRUE))
There's two common formats for chromosome:
chr1 vs. 1
We need to standardise this.