extract_depth {onemap}

Extract allele counts of progeny and parents of vcf file

Description

Uses vcfR package and onemap object to generates list of vectors with reference allele count and total counts for each marker and genotypes included in onemap object (only available for biallelic sites)

Usage

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

Arguments

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 allele counts informations, the implemented are: AD, DPR, GQ, PL, GL. AD and DPR return a list with allele depth information. GQ returns a matrix with error probability for each genotype. PL return a data.frame with genotypes probabilities for every genotype.

parent1

parent 1 identification in vcfR object

parent2

parent 2 identification in vcfR object

f1

if your cross type is f2, you must define the F1 individual

recovering

TRUE/FALSE, if TRUE evaluate all markers from vcf file, if FALSE evaluate only markers in onemap object

Value

list containing the following components:

palt

a matrix with parent 1 and 2 alternative allele counts.

pref

a matrix with parent 1 and 2 reference allele counts.

psize

a matrix with parent 1 and 2 total allele counts.

oalt

a matrix with progeny alternative allele counts.

oref

a matrix with progeny reference allele counts.

osize

a matrix with progeny total allele 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 inputted

Author(s)

Cristiane Taniguti, [e-mail]