extractGeneExpression {IsoformSwitchAnalyzeR} | R Documentation

## Extract raw gene counts or abundances from a switchAnalyzeRlist object.

### Description

Extract replicate gene raw unnormalised counts or expression from a switchAnalyzeRlist object using all the annotation fixes employed in creating the switchAnalyzeRlist.

### Usage

    extractGeneExpression(
        switchAnalyzeRlist,
        extractCounts = TRUE,
        addGeneNames = TRUE,
        addIdsAsColumns = TRUE
    )

### Arguments

`switchAnalyzeRlist` | A `switchAnalyzeRlist` object.
`extractCounts` | A logic to indicate whether to extract raw unnormalised counts (if TRUE, default) or expression estimates (if FALSE).
`addGeneNames` | A logic to indicate whether to add gene_names to the expression matrix (if TRUE, default) or not (if FALSE).
`addIdsAsColumns` | A logic to indicate whether to add the gene identifiers to the data.frame as collumns (if TRUE, default) or rownames (if FALSE).

### Details

The count matrix obtained if `extractCounts=TRUE` is the same as would be obtained by running tximport with `countsFromAbundance="scaledTPM" which are suitable both for analysis of differential expression and usage.`

### Value

A data.frame with the replicate count/abundance estimates as well as gene_id (and gene_name if `extractCounts=TRUE`)

### Author(s)

Kristoffer Vitting-Seerup

### References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

### Examples

    data("exampleSwitchList")

    ### Raw count matrix
    geneCountMatrix <- extractGeneExpression(
        exampleSwitchList,
        extractCounts = TRUE
    )

    ### Raw count matrix - with ids as rownames instead of columns
    geneCountMatrix <- extractGeneExpression(
        exampleSwitchList,
        extractCounts = TRUE,
        addIdsAsColumns = FALSE
    )

    ### Abundance matrix
    geneExpresionMatrix <- extractGeneExpression(
        exampleSwitchList,
        extractCounts = FALSE
    )

[Package IsoformSwitchAnalyzeR version 1.14.1 Index]