R: Function filter genotypes by genotype probability

filter_prob {onemap}

R Documentation

Function filter genotypes by genotype probability

Function filter genotypes by genotype probability

filter_prob(onemap.obj = NULL, threshold = 0.8, verbose = TRUE)

`onemap.obj`	an object of class `onemap`.
`threshold`	a numeric from 0 to 1 to define the threshold for the probability of the called genotype (highest probability)
`verbose`	If `TRUE`, print tracing information.

An object of class onemap, i.e., a list with the following components:

`geno`	a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.
`n.ind`	number of individuals.
`n.mar`	number of markers.
`segr.type`	a vector with the segregation type of each marker, as `strings`.
`segr.type.num`	a vector with the segregation type of each marker, represented in a simplified manner as integers, i.e. 1 corresponds to markers of type `"A"`; 2 corresponds to markers of type `"B1.5"`; 3 corresponds to markers of type `"B2.6"`; 4 corresponds to markers of type `"B3.7"`; 5 corresponds to markers of type `"C.8"`; 6 corresponds to markers of type `"D1"` and 7 corresponds to markers of type `"D2"`. Markers for F2 intercrosses are coded as 1; all other crosses are left as `NA`.
`input`	the name of the input file.
`n.phe`	number of phenotypes.
`pheno`	a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.
`error`	matrix containing HMM emission probabilities

Cristiane Taniguti, chtaniguti@tamu.edu


  data(onemap_example_out)
  filt_obj <- filter_prob(onemap_example_out, threshold=0.8)

[Package onemap version 3.0.0 Index]