CTSStoGenes: Make a gene expression table.

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

Make a gene expression table.

Description

Add a gene expression table in the GeneExpSE experiment slot of an annotated CAGEexp object.

Usage

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(), quickEnhancers(), resetCAGEexp(), summariseChrExpr()

Other CAGEr gene expression analysis functions: GeneExpDESeq2(), ranges2genes()

Examples

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

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.