calcSupport {CAGEfightR} | R Documentation

## Calculate support of CAGE data.

### Description

Calculate the number of samples expression a feature above a certain level. This number is refered to as the 'support'.

### Usage

    calcSupport(object, inputAssay = "counts", outputColumn = "support",
      unexpressed = 0)

### 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 support values.
`unexpressed` | numeric: Support will be calculated based on features larger than this cutoff.

### Value

object with support added as a column in rowRanges.

### See Also

Other Calculation functions: `calcBidirectionality`, `calcComposition`, `calcPooled`, `calcShape`, `calcTPM`, `calcTotalTags`, `subsetByBidirectionality`, `subsetByComposition`, `subsetBySupport`

### Examples

    data(exampleUnidirectional)

    # Count samples with at at least a single tags
    exampleUnidirectional <- calcSupport(exampleUnidirectional,
                                         inputAssay='counts',
                                         unexpressed=0)

    # Count number of samples with more than 1 TPM and save as a new column.
    exampleUnidirectional <- calcTPM(exampleUnidirectional,
                                     totalTags = 'totalTags')
    exampleUnidirectional <- calcSupport(exampleUnidirectional,
                                         inputAssay='TPM',
                                         unexpressed=1,
                                         outputColumn='TPMsupport')

[Package CAGEfightR version 1.6.0 Index]