normalize_counts: Perform a simple normalization of a count table.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Perform a simple normalization of a count table.

Description

This provides shortcut interfaces for normalization functions from deseq2/edger and friends.

Usage

normalize_counts(data, design = NULL, method = "raw", ...)

Arguments

data	Matrix of count data.
design	Dataframe describing the experimental design. (conditions/batches/etc)
method	Normalization to perform: 'sf|quant|qsmooth|tmm|upperquartile|tmm|rle' I keep wishy-washing on whether design is a required argument.
...	More arguments might be necessary.

Value

Dataframe of normalized(counts)

See Also

[edgeR] [limma] [DESeq2] [preprocessCore] [BiocGenerics]

Examples

## Not run: 
 norm_table = normalize_counts(count_table, design = design, norm='qsmooth')

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.