adjustDataset {phantasus}R Documentation

Adjust dataset

Description

Adjust dataset

Usage

adjustDataset(es, scaleColumnSum = NULL, log2 = FALSE,
  onePlusLog2 = FALSE, inverseLog2 = FALSE,
  quantileNormalize = FALSE, zScore = FALSE, robustZScore = FALSE,
  sweep = NULL)

Arguments

es

Expression set to perform adjustment on

scaleColumnSum

perform sum scaling of columns (default FALSE)

log2

perform logarithm2 adjustment (default FALSE)

onePlusLog2

perform log2(1+x) adjustment (default FALSE)

inverseLog2

perform 2^x adjustment (default FALSE)

quantileNormalize

perform quantile normalization (default FALSE)

zScore

perform zScore adjustment: subtract mean, divide by std (default FALSE)

robustZScore

perform robustZScore adjustment: subtract median, divide by MAD (default FALSE)

sweep

perform sweep adjustment on rows/columns (default FALSE)

Value

Nothing. Adjusted dataset will be assigned as ES in global environment

Examples

## Not run: 
es <- gseGSE('GSE53986')[[1]]
adjustDataset(es, log2 = T, quantileNormalize = T)

## End(Not run)


[Package phantasus version 1.4.0 Index]