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Applies normalization methods to given data set

applyNormalization.Rd

Applies single or multiple normalization methods to the given data. Available methods are:

  • Total Count (TC)

  • Upper Quartile (UQ)

  • Median (median)

  • Trimmed Median of Means (TMM)

  • DESeq

  • PoissonSeq

  • Quantile Normalization (QN)

  • Remove Unwanted Variation (RUVg, RUVr, and RUVs)

Usage

applyNormalization(
  data,
  groups = rep(0, ncol(data)),
  method = c("TC", "UQ", "median", "TMM", "DESeq", "PoissonSeq", "QN", "RUV")
)

Arguments

data

Un-normalized count data set of shape p x n, where p is the number of markers n is the number of samples.

groups

Vector of length n that maps the samples to sample groups.

method

Vector of normalization methods that are applied to the data. Available methods are: c("TC", "UQ", "median", "TMM", "DESeq", "PoissonSeq", "QN", "RUV"). Select one or multiple methods. By default all normalization methods will be applied.

Value

List of normalized read counts for selected normalization methods.

Details

If different groups or conditions are present in the data, the groups vector must provide a group label for each sample and, thus, maps each sample to a sample group (condition). If "RUV" normalization is applied to the data, groups must be provided; otherwise, providing sample groups is optional.