MissingRate: Sample missing rate check with SeqSQC object input file.

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

Sample missing rate check with SeqSQC object input file.

Description

Function to calculate sample missing rate and to identify sample outlier with high missing rate (> 0.1).

Usage

MissingRate(seqfile, remove.samples = NULL)

Arguments

seqfile	SeqSQC object, which includes the merged gds file for study cohort and benchmark.
remove.samples	a vector of sample names for removal from missing rate check. Could be problematic samples identified from other QC steps, or user-defined samples.

Details

The value of the outlier column is set to NA for benchmark samples.

Value

a data frame with sample name, sample missing rate, and an indicator of whether the sample has a missing rate greater than 0.1.

Author(s)

Qian Liu [e-mail]

Examples

load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
gfile <- system.file("extdata", "example.gds", package="SeqSQC")
seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile))
seqfile <- MissingRate(seqfile, remove.samples=NULL)
res.mr <- QCresult(seqfile)$MissingRate
tail(res.mr)

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