permuteDist: permuteDist

In ruqianl/comapr: Crossover analysis and genetic map construction

permuteDist

Description

Permutation test of two sample groups

Usage

permuteDist(co_gr, B = 100, mapping_fun = "k", group_by)

Arguments

co_gr	GRanges or RangedSummarizedExperiment object that contains the crossover counts for each marker interval across all samples. Returned by countCOs
B	integer the number of sampling times
mapping_fun	character default to "k" (kosambi mapping function). It can be one of the mapping functions: "k","h"
group_by	the prefix for each group that we need to generate distributions for(only when co_gr is a GRanges object). Or the column name for 'colData(co_gr)' that contains the group factor (only when co_gr is a RangedSummarizedExperiment object)

Details

It shuffles the group labels for the samples and calculate a difference between two groups after shuffling.

Value

A list of three elements. 'permutes' of length B with numeric differences of permuted group differences,'observed_diff' the observed genetic distances of two groups, 'nSample', the number of samples in the first and second group.

Author(s)

Ruqian Lyu

Examples

data(coCount)
perms <- permuteDist(coCount, group_by = "sampleGroup",B=10)

ruqianl/comapr documentation built on Oct. 27, 2023, 5:12 a.m.