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

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

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)

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