normalize: normalize a BioData::R6 object

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

normalize the expression data (sample wise) using DEseq2

normalize the expression data by subsampling as described in PMID 24531970

constructor that has to be implemented for a generic BioData This generic version was meant for array data and I have not had the need nor time to implement this part.

Usage

normalize(object, ..., name = NULL)

## S4 method for signature 'SingleCells'
normalize(object, reads = 600, force = FALSE, name = NULL)

## S4 method for signature 'MicroArray'
normalize(object, to = NULL, name = NULL)

Arguments

name	the name of the new object
reads	the required read depth
force	re-normalize this object (default FALSE)
to	a numeric vector to normalize the samples to. Has to have the same length as are columns in the data table
readCounts	The number of reads from each bam file or another value you want to normalize the data to
x	the MicoArray::BioData::R6 object

Value

the normalized data set (original data stored in NGS$raw

the normalized data set (original data stored in slot 'raw'

Functions

• normalize,SingleCells-method: a SingleCells::BioData::R6 object using subsampling

• normalize,MicroArray-method: normalize a MicoArray::BioData::R6 object using quantile normalization

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.