metaX (version 1.4.0)

autoRemoveOutlier: Automatically detect outlier samples

Description

Automatically detect outlier samples

Usage

autoRemoveOutlier(para, outTol = 1.2, pcaMethod = "svdImpute", valueID = "valueNorm", scale = "none", center = FALSE, ...)

Arguments

para

A metaXpara object

outTol

A factor to define the outlier tolerance, default is 1.2

pcaMethod

See pca in pcaMethods

valueID

The name of the column which will be used

scale

Scaling, see pca in pcaMethods

center

Centering, see pca in pcaMethods

...

Additional parameter

Value

The name of outlier samples

Examples

para <- new("metaXpara")
pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
sampleListFile(para) <- sfile
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
rs <- autoRemoveOutlier(para,valueID="value")