Drop a of set SNPs from a SNPdata object

Source: R/drop_snps.R

Drop a of set SNPs from a SNPdata object

drop_snps(
  snpdata,
  snp_to_be_dropped = NULL,
  chrom = NULL,
  start = NULL,
  end = NULL
)

Arguments

snpdata

The input SNPdata object

snp_to_be_dropped

A data frame with 2 columns: "Chrom" and "Pos".

chrom

The chromosome from which loci should be dropped

start

The starting position of the region to be discarded

end

The end position of the region to be discarded

Value

A SNPdata object where the specified SNPs have been removed.

Details

When 'snp_to_be_dropped' is not NULL (i.e. the genomic coordinates of snps to be removed are in a data frame), then the rest of the arguments can be ignored or set to NULL (chrom = NULL, start = NULL, end = NULL)

Examples

if (FALSE) { # \dontrun{
  snpdata <- drop_snps(
    snpdata,
    snp_to_be_dropped = NULL,
    chrom             = "Pf3D7_05_v3",
    start             = 100,
    end               = 500
  )
 } # }