filter_plink.pedmap: filter_plink.pedmap

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

filter_plink.pedmap

Description

used for filtration of p.link

Usage

filter_plink.pedmap(x,
                    mode = c("POS", "type", "both"),
                    Chr = Chr, start = start, end = end,
                    gff = gff, type = type, cusTyp = cusTyp,
                    geneID = geneID)

Arguments

x	a list stored the p.link information
mode	filtration mode, one of c("POS", "type", "both")
Chr	the chromosome name, need if mode set as POS or both
start, end	numeric, the range of filtration, and the start should smaller than end
gff	the imported gff object
type	should be in unique(gff$type), usually as "CDS", "genome".
cusTyp	if type set as custom, then cusTyp is needed
geneID	geneID

Value

list, similar with x, but filtered

Examples

   pedfile <- system.file("extdata",
                          "snp3kvars-CHR8-25947258-25951166-plink.ped",
                          package = "geneHapR")
   mapfile <- system.file("extdata",
                          "snp3kvars-CHR8-25947258-25951166-plink.map",
                          package = "geneHapR")
   p.link <- import_plink.pedmap(pedfile = pedfile, mapfile = mapfile,
                                 sep_map = "\t", sep_ped = "\t")
   p.link <- filter_plink.pedmap(p.link, mode = "POS",
                                 Chr = "chr08", start = 25948004,
                                 end = 25949944)
   hapResult <- plink.pedmap2hap(p.link, hapPrefix = "H",
                                 hetero_remove = TRUE,
                                 na_drop = TRUE)

geneHapR documentation built on May 29, 2024, 11:59 a.m.