adjustDataset: Adjust dataset

In baba-beda/morpheusR: Visual and interactive gene expression analysis

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)

baba-beda/morpheusR documentation built on Oct. 10, 2024, 1:35 a.m.