extract_depth: Extract allele counts of progeny and parents of vcf file
In Cristianetaniguti/genotyping4onemap: genotyping4onemap

Description Usage Arguments Value Author(s)

View source: R/extract_depth.R

Uses vcfR package and onemap object to generates list of vectors with reference alelle count and total counts for each marker and genotypes included in onemap object

extract_depth(
  vcfR.object = NULL,
  onemap.object = NULL,
  vcf.par = c("GQ", "AD", "DPR"),
  parent1 = "P1",
  parent2 = "P2",
  f1 = "F1",
  mean_phred = 20,
  recovering = FALSE
)

`vcfR.object`	object output from vcfR package
`onemap.object`	onemap object output from read_onemap, read_mapmaker or onemap_read_vcf function
`vcf.par`	vcf format field that contain alelle counts informations, usually AD and DPR
`parent1`	parent 1 identification in vcfR object
`parent2`	parent 2 identification in vcfR objetc
`recovering`	TRUE/FALSE, if TRUE avaliate all markers from vcf file, if FALSE avaliate only markers in onemap object

list containing the following components:

`palt`	a `matrix` with parent 1 and 2 alternative alelle counts.
`pref`	a `matrix` with parent 1 and 2 reference alelle counts.
`psize`	a `matrix` with parent 1 and 2 total alelle counts.
`oalt`	a `matrix` with progeny alternative alelle counts.
`oref`	a `matrix` with progeny reference alelle counts.
`osize`	a `matrix` with progeny total alelle counts.
`n.mks`	total number of markers.
`n.ind`	total number of individuals in progeny.
`inds`	progeny individuals identification.
`mks`	markers identification.
`onemap.object`	same onemap.object inputed