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

filterGenotypeTableSites(
  tasObj,
  siteMinCount = 0,
  siteMinAlleleFreq = 0,
  siteMaxAlleleFreq = 1,
  minHeterozygous = 0,
  maxHeterozygous = 1,
  removeMinorSNPStates = FALSE,
  removeSitesWithIndels = FALSE,
  siteRangeFilterType = c("none", "sites", "position"),
  startSite = NULL,
  endSite = NULL,
  startChr = NULL,
  startPos = NULL,
  endChr = NULL,
  endPos = NULL,
  gRangesObj = NULL,
  chrPosFile = NULL,
  bedFile = NULL
)

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.

removeMinorSNPStates

Remove minor SNP states. Defaults to FALSE.

removeSitesWithIndels

Remove sites containing an indel (+ or -). Defaults to FALSE.

siteRangeFilterType

True if filtering by site numbers. False if filtering by chromosome and position. Options are none, sites, or position. Defaults to none.

startSite

The start site. Defaults to 0.

endSite

The end site. Defaults to 0.

startChr

Start chromosome for site filtration range if position is chosen from siteRangeFilterType. Needs end chromosome (endChr) to work.

startPos

Physical start position (bp) for filtration range if position is chosen from siteRangeFilterType. If NULL, the first physical position in the data set will be chosen.

endChr

End chromosome for site filtration range if position is chosen from siteRangeFilterType. Needs start chromosome (endChr) to work.

endPos

Physical end position (bp) for filtration range if position is chosen from siteRangeFilterType. If NULL, the last physical position in the data set will be chosen.

gRangesObj

Filter genotype table by GenomicRanges object. If this parameter is selected, you cannot utilize the parameters, chrPosFile or bedFile. Defaults to NULL.

chrPosFile

An optional chromosome position file path of character class. Defaults to NULL. Note: a chromosome position file must contain correct formatting (e.g. a two column file with the header of c("Chromosome", "Position")).

bedFile

An optional BED coordinate file path of character class. Defaults to NULL.

Value

Returns an object of TasselGenotypePhenotype class.