lumiR.batch: Read BeadStudio output files in batch

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

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

Usage

lumiR.batch(fileList, convertNuID = TRUE, lib.mapping = NULL, detectionTh = 0.01, QC = TRUE, transform = c('none', 'vst', 'log2', 'cubicRoot'), sampleInfoFile = NULL, verbose = TRUE, ...)

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.mapping	same as lumiR parameter lib.mapping (optional)
detectionTh	the p-value threshold of determining detectability of the expression. See more details in lumiQ
QC	determine whether to do quality control assessment after read in the data.
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)
verbose	a boolean to decide whether to print out some messages
...	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". The sample ID column can also be found in the "Samples Table.txt" file output by BeadStudio. Another "Label" column (if provided) will be used as the 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, sampleInfoFile='sampleInfo.txt')

lumi documentation built on Nov. 8, 2020, 5:27 p.m.