filter_hmp: filter variants in hapmap format

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

filter variants in hapmap format

Description

filter variants in hapmap format

Usage

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

Arguments

x	genotype dataset in hapmap format, object of data.frame class
mode	filter mode, one of "POS", "type", "both"
Chr	chromosome name, needed if mode set to "POS" or "both"
start	start position, needed if mode set to "POS" or "both"
end	end position, needed if mode set to "POS" or "both"
gff	object of GRanges class, genome annotations imported by import_gff()
type	filter type, needed if mode set to "type" or "both", one of "CDS", "exon", "gene", "genome", "custom", if type was set to "custom", then custom_type is needed.
cusTyp	character vector, custom filter type, needed if type set to "custom"
geneID	gene ID

Examples

# create a dataset of genotype in hapmap format
hmp <- hap2hmp(hapResult);

# example
hmp <- filter_hmp(hmp, mode = "POS",
                      Chr = "scaffold_1", start = 4100, end = 5000)

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