calculateGeneExpressionValues: Calculates the gene expression values by using a matrix of...

In CasedUgr/KnowSeq: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Calculates the gene expression values by using a matrix of counts from RNA-seq.

Description

Calculates the gene expression values by using a matrix of counts from RNA-seq. Furthermore, the conversion from Ensembl IDs to genes names is performed by default, but can be changed with the parameter genesNames.

Usage

calculateGeneExpressionValues(
  countsMatrix,
  annotation,
  genesNames = TRUE,
  notHuman = FALSE,
  notHumanGeneLengthCSV = "",
  Ensembl_ID = TRUE
)

Arguments

countsMatrix	The original counts matrix returned by countsToMatrix function or a matrix with the gene Ensembl ID in the rows and the samples in the columns that contains the count values.
annotation	A matrix that contains the Ensembl IDs, the gene name and the percentage gene gc content for the genes available in the expression matrix. This annotation could be extracted from the function getGenesAnnotation.
genesNames	A boolean variable which indicates if the rownames of the expression matrix are the genes Names (Symbols) or the ensembl IDs.
notHuman	A boolean variable which indicates if the gene length file is the default gene length human file or another file indicated by parameter.
notHumanGeneLengthCSV	Path to the CSV file that contains the gene length of the specie to use.
Ensembl_ID	A boolean variable which indicate if the counts matrix contains Ensembl_ID(TRUE) or genes names(FALSE).

Value

A matrix that contains the gene expression values. The rownames are the genes names or the Ensembl IDs and the colnames are the samples.

Examples

dir <- system.file("extdata", package="KnowSeq")
load(paste(dir,"/expressionExample.RData",sep = ""))

expressionMatrix <- calculateGeneExpressionValues(countsMatrix,myAnnotation, genesNames = TRUE)

CasedUgr/KnowSeq documentation built on Aug. 16, 2022, 6:19 a.m.