applyNormalization: Applies normalization methods to given data set

In LXQin/DANA: Data-driven Normalization Assessment for miRNA-Seq Data

Applies normalization methods to given data set

Description

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.

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.

Value

List of normalized read counts for selected normalization methods.

LXQin/DANA documentation built on March 7, 2024, 3:24 a.m.