calcSupport: Calculate support of CAGE data.

Description Usage Arguments Value See Also Examples

View source: R/calc.R

Description

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

Usage

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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

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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')

MalteThodberg/CAGEfightR documentation built on Oct. 24, 2018, 12:10 p.m.