base2num {Hapi} | R Documentation |
Convert base (A/T/C/G) coded genotype to numeric (0/1) coded
base2num(gmt, ref, alt)
gmt |
a dataframe of genotype data of gamete cells |
ref |
a character represents reference allele |
alt |
a character represents alternative allele |
a dataframe containing converted genotype
Ruidong Li
ref <- sample(c('A','T'),500, replace=TRUE)
alt <- sample(c('C','G'),500, replace=TRUE)
gmt <- data.frame(chr=rep(1,500), pos=seq_len(500),
ref=ref, alt=alt, gmt1=ref, gmt2=alt, gmt3=ref,
gmt4=ref, gmt5=c(alt[1:250], ref[251:500]),
stringsAsFactors = FALSE)
gmtDa <- base2num(gmt=gmt[5:9], ref=ref, alt=alt)