Update Format_data.R

YangLabHKUST · Aug 8, 2022 · 51cde60 · 51cde60
1 parent bd0dd1d
commit 51cde60
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/R/Format_data.R b/R/Format_data.R
@@ -240,6 +240,7 @@ format_data <- function(dat,
  # remove SNP with allele freqcy less than min_freq
  dat[is.na(dat$freq),"freq"] = 0.5
  dat = dat[dat$freq > min_freq & dat$freq < (1-min_freq), ]
+ message("Remove SNPs with MAF less than", min_freq, ", remaining ", nrow(dat), " SNPs.")
  }