filter_segregation {mappoly}

Filter markers based on chi-square test

Description

This function filter markers based on p-values of a chi-square test. The chi-square test assumes that markers follow the expected segregation patterns under Mendelian inheritance, random chromosome bivalent pairing and no double reduction.

Usage

filter_segregation(input.obj, chisq.pval.thres = NULL, inter = TRUE)

Arguments

input.obj

name of input object (class mappoly.data)

chisq.pval.thres

p-value threshold used for chi-square tests (default = Bonferroni aproximation with global alpha of 0.05, i.e., 0.05/n.mrk)

inter

if TRUE (default), plots distorted vs. non-distorted markers

Value

An object of class mappoly.chitest.seq which contains a list with the following components:

keep

markers that follow Mendelian segregation pattern

exclude

markers with distorted segregation

chisq.pval.thres

threshold p-value used for chi-square tests

data.name

input dataset used to perform the chi-square tests

Author(s)

Marcelo Mollinari, [e-mail]

Examples

mrks.chi.filt <- filter_segregation(input.obj = tetra.solcap,
                                    chisq.pval.thres = 0.05/tetra.solcap$n.mrk,
                                    inter = TRUE)
seq.init <- make_seq_mappoly(mrks.chi.filt)