filterGenotypeTableSites: Filter genotype table by sites
In maize-genetics/rTASSEL: R Front-End for TASSEL

filterGenotypeTableSites

R Documentation

Filter genotype table by sites

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,
  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`.