dot-rowNormFact: Obtain normalization factor (main)

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

Obtain normalization factor (main)

Description

This function was designed to obtain normalization factors.

Usage

.rowNormFact(
  dat,
  combOfN,
  comUse,
  method = "median",
  refLi = NULL,
  refGrp = NULL,
  proportMode = TRUE,
  minQuant = NULL,
  maxFact = 10,
  omitNonAlignable = FALSE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat	(matrix) .. init data, smay be parse matrix with numerous NA
combOfN	(matrix) .. # matrix of index for all sub-groups (assumed as sorted)
comUse	(list) .. index of complete lines for each col of combOfN
method	(character) may be "mean","median" (plus "NULL","none"); When NULL or 'none' is chosen the input will be returned as is
refLi	(NULL or numeric) allows to consider only specific lines of 'dat' when determining normalization factors (all data will be normalized)
refGrp	(integer) Only the columns indicated will be used as reference, default all columns (integer or colnames)
proportMode	(logical) decide if normalization should be done by multiplicative or additive factor
minQuant	(numeric) optional filter to set all values below given value as NA
maxFact	(numeric, length=2) max normalization factor
omitNonAlignable	(logical) allow omitting all columns which can't get aligned due to sparseness
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) This function allows easier tracking of messages produced

Value

This function returns a matrix of column-indexes complementing (nCombin rows)

See Also

rowNormalize

Examples

ma1 <- matrix(11:41, ncol=3)

wrMisc documentation built on Sept. 11, 2024, 6:10 p.m.