rf_snp_filter_onemap {onemap}

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, [e-mail]

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))