glycanr (version 0.4.0)

quantilenorm: 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

Value

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

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)

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. 10.1093/bioinformatics/19.2.185

Examples

# NOT RUN {
data(mpiu)
if(requireNamespace("preprocessCore", quietly=TRUE)){
  mpiun <- quantilenorm(mpiu)
  head(mpiun)

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