wrMisc (version 1.15.3.1)

.rowNormFact: 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
)

Value

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

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

See Also

rowNormalize

Examples

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