featureTableNormalize: featureTableNormalize

In mjhelf/Mosaic: Metaboseek platform

featureTableNormalize

Description

Function to normalize data in a matrix.

Usage

featureTableNormalize(
  mx,
  raiseZeros = NULL,
  log = NULL,
  normalize = FALSE,
  normalizationFactors = NULL,
  threshold = NULL,
  thresholdMethod = NULL
)

## S4 method for signature 'data.frame'
FTNormalize(object, intensityCols, logNormalized = FALSE)

Arguments

mx	a matrix of numeric (intensity) values
raiseZeros	if not NULL, values of 0 will be raised to a level defined by a character string. "min" will raise all zeros to the lowest non-zero value in mx - normalization is done after this step so that the zero-replacement values will ary across samples (which is needed for t-tests, etc.)
log	if not NULL, log10 will be applied to values in mx
normalize	if not NULL, column values will be normalized by column averages
normalizationFactors	vector of length(ncol(mx)) with factors to apply to each column for normalization.
threshold	numeric(1).
thresholdMethod	if not NULL, removes all rows in mx in which no value is above threshold
object	a data.frame
intensityCols	selected columns (with intensity values)
logNormalized	if TRUE, applies a log10 to intensity values after normalization

Value

mx, normalized so that all columns have the same mean value which is also the mean of all values in mx

mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.