doc/remove_snp.md

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

NAME

drop_snps

USAGE

drop_snps(snpdata, snp.to.be.dropped=NA, chrom=NA, start=NA, end=NA)

DESCRIPTION

drop_snps is a function that removes a set of snps from the SNPdata object. the genomic coordinates of the loci to be removed could be given as a data frame with 2 columns: "Chrom" and "Pos" (in this case, the rest of the argument can be ignored or set to NA) or as a genomic region: chrom="Pf3D7_10_v3", start=100, end=500 (in this case, the snp.to.be.dropped argument can be ignored or set to NA)

OPTIONS

snpdata: an object of class SNPdata
snp.to.be.dropped: a data frame with 2 columns: Chrom and Pos
chrom: the chromosome to which to loci to be removed belong 
start: the starting position of the loci to be removed
end: the end position of the loci to be removed

RETURN

a SNPdata object where the corresponding loci of the specified genomic coordinates have been removed

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.