rf_snp_filter_onemap: Filter markers according with a two-points recombination...
In onemap: Construction of Genetic Maps in Experimental Crosses

rf_snp_filter_onemap

R Documentation

Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.

Description

Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.

Usage

rf_snp_filter_onemap(
  input.seq,
  thresh.LOD.rf = 5,
  thresh.rf = 0.15,
  probs = c(0.05, 1)
)

Arguments

`input.seq`	an object of class `onemap`.
`thresh.LOD.rf`	LOD score threshold for recombination fraction (default = 5)
`thresh.rf`	threshold for recombination fractions (default = 0.15)
`probs`	indicates the probability corresponding to the filtering quantiles. (default = c(0.05, 1))

Value

An object of class sequence, which is a list containing the following components:

`seq.num`	a `vector` containing the (ordered) indices of markers in the sequence, according to the input file.
`seq.phases`	a `vector` with the linkage phases between markers in the sequence, in corresponding positions. `-1` means that there are no defined linkage phases.
`seq.rf`	a `vector` with the recombination frequencies between markers in the sequence. `-1` means that there are no estimated recombination frequencies.
`seq.like`	log-likelihood of the corresponding linkage map.
`data.name`	object of class `onemap` with the raw data.
`twopt`	object of class `rf_2pts` with the 2-point analyses.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

Examples


 data("vcf_example_out")
 twopts <- rf_2pts(vcf_example_out)
 seq1 <- make_seq(twopts, which(vcf_example_out$CHROM == "1"))
filt_seq <- rf_snp_filter_onemap(seq1, 20, 0.5, c(0.5,1))

onemap documentation built on Nov. 26, 2022, 9:05 a.m.