MissingRate {SeqSQC} | R Documentation

## 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 qliu7@buffalo.edu

### 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)

[Package SeqSQC version 1.2.0 Index]