norm.RUV: Normalization By Remove Unwanted Variation (RUV)

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

Normalization By Remove Unwanted Variation (RUV)

Description

Normalize the dataset using RUV. All three sub-methods (RUVg, RUVs, and RUVr) can be used.

Usage

norm.RUV(raw, groups, method = c("RUVg", "RUVs", "RUVr"))

Arguments

raw	Raw read count matrix (rows = genes, cols = samples).
groups	Sample groups (subtypes)

Value

A list with the following elements:

dataNormalized

Normalized read counts.

adjustFactor

Adjusting factors for adjusting the design matrix.

list, containing dat.normed (normalized dataset), and the adjust.factor (adjusting factors) for the design matrix. The normalized dataset could only used for exploration, and adjusting factors are recommended as a covariate in the downstream analysis.

References

RUVSeq Tutorial

Examples

## Not run: 
  normCounts <- norm.RUV(rawCounts, groups, method="RUVg")

## End(Not run)

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