normalise: Normalise single cells from 'RNAseq' object
In BPijuanSala/proSeq: Tools to preprocess RNA-seq data

Description Usage Arguments Value Author(s)

It normalises single cells from countsRaw slot within the RNAseq object provided. It follows Brennecke et al., Nature Methods, 2013.

normalise(object, cells = NULL, genes = NULL, genes.SizF = NULL,
  ercc.SizF = NULL)

## S4 method for signature 'RNAseq'
normalise(object, cells = NULL, genes = NULL,
  genes.SizF = NULL, ercc.SizF = NULL)

`object`	`RNAseq` object.
`cells`	vector of cells to normalise. Default: NULL. This will first look at the `cellsFailQC` slot and if empty, it will take all the cells in the `countsRaw` slot
`genes`	vector of genes to normalise. Default: NULL (It will take all the genes of the `countsRaw` slot).
`genes.SizF`	Genes to use to compute genes size factors for each cell. Default: Vector of "genes" that are not ERCCs.
`ercc.SizF`	ERCCs to use to compute ERCC size factors for each cell. Default: Vector of "erccs".

List with normalised counts Matrix (countsNorm) and size factors for biological genes (sizeFactorsGenes) and spike-ins (sizeFactorsSpikeIn). countsNorm should be stored in object@countsNorm slot and the size factors should be stored in object@CellsSizeFac slot as a list (with the two types of size factors).

Blanca Pijuan Sala.

BPijuanSala/proSeq documentation built on May 30, 2019, 11:47 p.m.