filterGenotypeTableSites: Filter genotype table by sites

In maize-genetics/bioconductor_test: R front-end for TASSEL

Description

This function will filter R objects of TasselGenotypePhenotype class containing genotype tables. The parameters for this function are derived from TASSEL's FilterSiteBuilder plugin.

Usage

filterGenotypeTableSites(tasObj, siteMinCount = 0,
  siteMinAlleleFreq = 0, siteMaxAlleleFreq = 1, minHeterozygous = 0,
  maxHeterozygous = 1, siteRangeFilterType = "NONE", startSite = 0,
  endSite = 0)

Arguments

tasObj	An object of class TasselGenotypePenotype.
siteMinCount	Site minimum count of alleles not unknown. Can range from 0 to inf. Defaults to 0.
siteMinAlleleFreq	Site minimum minor allele frequency. Can range from 0 to 1.0. Defaults to 0.0.
siteMaxAlleleFreq	Site maximum minor allele frequency. Can range from 0 to 1.0. Defaults to 1.0.
minHeterozygous	Min heterozygous proportion. Can range from 0 to 1.0. Defaults to 0.0.
maxHeterozygous	Max heterozygous proportion. Can range from 0 to 1.0. Defaults to 1.0.
siteRangeFilterType	True if filtering by site numbers. False if filtering by chromosome and position. Options are NONE, SITES, or POSITIONS. Defaults to NONE.
startSite	The start site. Defaults to 0.
endSite	The end site. Defaults to 0.

Value

Returns an object of TasselGenotypePhenotype class.

maize-genetics/bioconductor_test documentation built on Nov. 4, 2019, 5:19 p.m.