filter_plink.pedmap | R Documentation |
used for filtration of p.link
filter_plink.pedmap(x,
mode = c("POS", "type", "both"),
Chr = Chr, start = start, end = end,
gff = gff, type = type, cusTyp = cusTyp,
geneID = geneID)
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 |
cusTyp |
if |
geneID |
geneID |
list, similar with x
, but filtered
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)
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