quantilenorm {glycanr}

Quantile Normalization of glycan data

Description

Returns glycans normalized with Quantile Normalization approach.

Usage

quantilenorm(d, grouping = FALSE, transpose = FALSE)

Arguments

d

data frame in long format containing glycan measurements

grouping

should data be normalized per groups

transpose

transpose the data prior to normalization

Details

Input data frame should have at least the following three columns:
- gid - representing a unique name of a sample
- glycan - representing glycan names
- value - representing measured values
and if the grouping argument is TRUE it should also have column:
- groups - representing groupings (e.g. IgG1, IgG2 and IgG4)

Value

Returns a data.frame with original glycan values substituted by normalized ones

Author(s)

Ivo Ugrina, Lucija Klarić

References

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P.:
A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance.
Bioinformatics 19(2), p. 185-193, 2003.
doi: 10.1093/bioinformatics/19.2.185

Examples

data(mpiu)
if(requireNamespace("preprocessCore", quietly=TRUE)){
  mpiun <- quantilenorm(mpiu)
  head(mpiun)

  # transpose (change) subjects and measurements
  mpiunt <- quantilenorm(mpiu, transpose=TRUE)
  head(mpiunt)
}