asBigMatrix-methods: convert the data matrix in the assayData of a ExpressionSet...

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

Description

convert the data matrix in the assayData of a ExpressionSet as BigMatrix

Usage

## S4 method for signature 'ExpressionSet'
asBigMatrix(object, rowInd=NULL, colInd=NULL, nCol=NULL, dimNames=NULL, saveDir='.', savePrefix=NULL, ...)

Arguments

object	an object of ExpressionSet or its inherited class
rowInd	the subset of row index
colInd	the subset of column index
nCol	the number of columns of the data, which can be larger than the real data dimension. It is designed for adding future data.
dimNames	the dimension names, which is a list of two character vectors (rownames and colnames)
saveDir	the parent directory to save the BigMatrix data files
savePrefix	the folder name prefix of the directory to save the BigMatrix data files. The fold name will be like this: paste(savePrefix, '_bigmat', sep=”)
...	optional arguments to BigMatrix

Details

This function does not work in Windows because the dependent package bigmemoryExtras does not support it. In order to make lumi package still compilation under Windows, I deliberately remove the dependency of bigmemoryExtras package. As a result, users need to manually load the bigmemoryExtras function before using this function.

The BigMatrix data files will be save in the directory file.path(saveDir, paste(savePrefix, '_bigmat', sep=”))

See Also

BigMatrix

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