filter_plink.pedmap {geneHapR}

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)