filterGT: filterGT

In ruqianl/comapr: Crossover analysis and genetic map construction

filterGT

Description

Filter markers or samples that have too many missing values

Usage

filterGT(geno, min_markers = 5, min_samples = 3)

## S4 method for signature 'matrix,numeric,numeric'
filterGT(geno, min_markers = 5, min_samples = 3)

## S4 method for signature 'GRanges,numeric,numeric'
filterGT(geno, min_markers = 5, min_samples = 3)

Arguments

geno	the genotype data.frame of markers by samples from output of function correctGT
min_markers	the minimum number of markers for a sample to be kept
min_samples	the minimum number of samples for a marker to be kept

Details

This function takes the geno data.frame and filter the data.frame by the provided cut-offs.

Value

The filtered genotype matrix

Author(s)

Ruqian Lyu

Examples

data(snp_geno_gr)
corrected_geno <- filterGT(snp_geno_gr, min_markers = 30,min_samples = 2)

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