normalise: Normalise single cells from 'RNAseq' object

Description Usage Arguments Value Author(s)

Description

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

Usage

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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)

Arguments

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".

Value

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

Author(s)

Blanca Pijuan Sala.


BPijuanSala/proSeq documentation built on Oct. 10, 2018, 7:20 p.m.