mappoly (version 0.2.3)

filter_segregation: 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.data, chisq.pval.thres = 1e-04, inter = TRUE)

Arguments

input.data

name of input object (class mappoly.data)

chisq.pval.thres

p-value threshold used for chi-square tests (default = 10e-05)

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

Examples

# NOT RUN {
mrks.chi.filt <- filter_segregation(input.data = tetra.solcap,
                                    chisq.pval.thres = 0.05/tetra.solcap$n.mrk,
                                    inter = TRUE)
seq.init<-make_seq_mappoly(mrks.chi.filt)

# }