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)
extract_depth(
vcfR.object = NULL,
onemap.object = NULL,
vcf.par = c("GQ", "AD", "DPR, PL", "GL"),
parent1 = "P1",
parent2 = "P2",
f1 = "F1",
recovering = FALSE
)
list containing the following components:
a matrix
with parent 1 and 2
alternative allele counts.
a matrix
with parent 1 and 2
reference allele counts.
a matrix
with parent 1 and 2
total allele counts.
a matrix
with progeny
alternative allele counts.
a matrix
with progeny
reference allele counts.
a matrix
with progeny
total allele counts.
total number of markers.
total number of individuals in progeny.
progeny individuals identification.
markers identification.
same onemap.object inputted
object output from vcfR package
onemap object output from read_onemap, read_mapmaker or onemap_read_vcf function
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.
parent 1 identification in vcfR object
parent 2 identification in vcfR object
if your cross type is f2, you must define the F1 individual
TRUE/FALSE, if TRUE evaluate all markers from vcf file, if FALSE evaluate only markers in onemap object
Cristiane Taniguti, chtaniguti@tamu.edu