writeEset: Exporting an ExpressionSet instance into 3 tabulated files...

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Exporting an ExpressionSet instance into 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', and 'variableMetadata.tsv'

Description

Note that the dataMatrix is transposed before export (e.g., the samples are written column wise in the 'dataMatrix.tsv' exported file).

Usage

writeEset(x, dirName, overwrite = FALSE, verbose = TRUE)

## S4 method for signature 'ExpressionSet'
writeEset(x, dirName, overwrite = FALSE, verbose = TRUE)

Arguments

x	An S4 object of class ExpressionSet
dirName	Character: directory where the tables should be written
overwrite	Logical: should existing files be overwritten?
verbose	Logical: should messages be printed?

Value

No object returned.

Examples

library(ptairData)
dirRaw <- system.file("extdata/exhaledAir", package = "ptairData")
exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", 
mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL )
exhaledPtrset<-detectPeak(exhaledPtrset,mz=c(21,59,77))
eset <- ptairMS::alignSamples(exhaledPtrset ) 
writeEset(eset, dirName = file.path(getwd(), "processed_dataset"))
unlink(file.path(getwd(), "processed_dataset"),recursive = TRUE)

camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.m.