lumiR.batch {lumi}R Documentation

Read BeadStudio output files in batch

Description

Read BeadStudio output files in batch and combine them as a single LumiBatch object

Usage

lumiR.batch(fileList, convertNuID = TRUE, lib = NULL, transform = c('none', 'vst', 'log2', 'cubicRoot'), sampleInfoFile = NULL, ...)

Arguments

fileList a vector of file names or a directory keeping the data files in the format of .csv
convertNuID determine whether convert the probe identifier as nuID
lib same as lumiR parameter lib (optional)
transform determine whether to do transform after input each file
sampleInfoFile a Tab-separated text file or a data.frame keeping the sample information (optional)
... other parameters used by lumiR

Details

The function basically call lumiR for individual files and then combine the returns. The sampleInfoFile parameter is optional. It provides the sample information (for phenoData slot in LumiBatch object), it is a Tab-separated text file. ID column is required. It represents sample ID, which is defined based on the column names of BeadStudio output file. For example, sample ID of column "1881436070_A_STA.AVG_Signal" is "1881436070_A_STA". Another Label column is optional, which is sampleNames of LumiBatch object. All information of sampleInfoFile will be directly added in the phenoData slot in LumiBatch object.

To save memory space in the case of reading large data set, we can do transformation using lumiT function right after input the data, and the information like se.exprs, beadNum will be removed from the LumiBatch object after transformation.

Value

A LumiBatch object which combines the individual LumiBatch object corresponding to each file

Author(s)

Pan Du

See Also

lumiR

Examples

## fileList <- c('file1.csv', 'file2.cvs')
## x.lumi <- lumiR.batch(fileList)


[Package lumi version 1.6.3 Index]