.normalize {wrMisc}

Main Normalization function

Description

This function aims to normalize a matrix or data.frame by columns. It assumes all checks have been done before calling this function.

Usage

.normalize(
  dat,
  meth,
  mode,
  param,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat

matrix or data.frame of data to get normalized

meth

(character) may be "mean","median","NULL","none", "trimMean", "rowNormalize", "slope", "exponent", "slope2Sections", "vsn"; When NULL or 'none' is chosen the input will be returned

mode

(character) may be "proportional", "additive"; decide if normalizatio factors will be applies as multiplicative (proportional) or additive; for log2-omics data mode="aditive" is suggested

param

(list) additional parameters

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allows easier tracking of messages produced

Value

This function returns a numeric vector

See Also

normalizeThis

Examples

aa <- matrix(1:12, ncol=3)
.normalize(aa,"median",mode="proportional",param=NULL)