problemList: Generate the problematic sample list.

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

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)

SeqSQC documentation built on Nov. 8, 2020, 5:03 p.m.