CTSStoGenes: Make a gene expression table.

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Add a gene expression table in the GeneExpSE experiment slot of an annotated CAGEexp object. CAGEset objects are not supported.

Usage

CTSStoGenes(object)

## S4 method for signature 'CAGEset'
CTSStoGenes(object)

## S4 method for signature 'CAGEexp'
CTSStoGenes(object)

Arguments

object

A CAGEexp object that was annotated with the annotateCTSS() function.

Value

The input object with the following modifications:

• A new geneExpMatrix experiment containing gene expression levels as a SummarizedExperiment object with one assay called counts, which is plain matrix of integers. (This plays better than Rle DataFrames when interfacing with downstream packages like DESeq2, and since the number of genes is limited, a matrix will not cause problems of performance.)

• New genes column data added, indicating total number of gene symbols detected per library.

• New unannotated column data added, indicating for each sample the number of counts that did not overlap with a known gene.

Author(s)

Charles Plessy

See Also

annotateCTSS().

Other CAGEr object modifiers: CustomConsensusClusters, aggregateTagClusters, annotateCTSS, clusterCTSS, cumulativeCTSSdistribution, getCTSS, normalizeTagCount, quantilePositions, summariseChrExpr

Other CAGEr gene expression analysis functions: GeneExpDESeq2, ranges2genes

Examples

CTSStoGenes(exampleCAGEexp)
all( librarySizes(exampleCAGEexp) -
     colSums(SummarizedExperiment::assay(GeneExpSE(exampleCAGEexp))) ==
     exampleCAGEexp$unannotated)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.