problemList: Generate the problematic sample list.

In Liubuntu/SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

Generate the problematic sample list.

Description

generate the problematic sample list from QC steps that have been done, and provide each problematic sample with a reason for removal (high missing rate, gender mismatch, inbreeding outlier, cryptic relationship or population outlier).

Usage

problemList(seqfile)

Arguments

seqfile

SeqSQC object with sample QC results.

Value

a list of 2 datasets: 1) a data frame with 2 columns: sample for problematic sample name, and remove.reason for the reason of removing the sample. 2) a data frame with 1 column sample for problematic samples to be removed.

Author(s)

Qian Liu [e-mail]

Examples

load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
problemList(seqfile)

Liubuntu/SeqSQC documentation built on April 12, 2024, 6:39 p.m.