rf_snp_filter_onemap function

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

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))

Returns

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.

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))

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu