problemList {SeqSQC} | R Documentation

## 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 qliu7@buffalo.edu

### Examples

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

[Package SeqSQC version 1.14.0 Index]