calcComposition {CAGEfightR} | R Documentation

## Calculate composition of CAGE data.

### Description

For every feature, count in how many samples it is expressed above a certain fraction (e.g. 10 percent) within a grouping, usually genes. This count is refered to as the 'composition' value.

### Usage

    calcComposition(
      object,
      inputAssay = "counts",
      outputColumn = "composition",
      unexpressed = 0.1,
      genes = "geneID"
    )

### Arguments

`object` | RangedSummarizedExperiment: CAGE data quantified at CTSS, cluster or gene-level.
`inputAssay` | character: Name of assay holding input expression values.
`outputColumn` | character: Name of column in rowRanges to hold composition values.
`unexpressed` | numeric: Composition will be calculated based on features larger than this cutoff.
`genes` | character: Name of column in rowData holding genes (NAs are not currently allowed.)

### Value

object with composition added as a column in rowData.

### See Also

Other Calculation functions: `calcBidirectionality()`, `calcPooled()`, `calcShape()`, `calcSupport()`, `calcTPM()`, `calcTotalTags()`, `subsetByBidirectionality()`, `subsetByComposition()`, `subsetBySupport()`

### Examples

    data(exampleUnidirectional)

    # Annotate clusters with geneIDs:
    library(TxDb.Mmusculus.UCSC.mm9.knownGene)
    txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
    exampleUnidirectional <- assignGeneID(exampleUnidirectional,
                                          geneModels=txdb,
                                          outputColumn='geneID',
                                          swap='thick')

    # Calculate composition values:
    exampleUnidirectional <- subset(exampleUnidirectional, !is.na(geneID))
    calcComposition(exampleUnidirectional)

    # Use a lower threshold
    calcComposition(exampleUnidirectional,
                    unexpressed=0.05,
                    outputColumn='lenientComposition')

[Package CAGEfightR version 1.12.0 Index]