symbolsToRanges {TCGAutils}R Documentation

Convert SummarizedExperiment elements with gene symbols to RangedSummarizedExperiment

Description

Convert SummarizedExperiment elements with gene symbols to RangedSummarizedExperiment

Usage

symbolsToRanges(obj, keep = FALSE)

Arguments

obj

A MultiAssayExperiment object obtained from curatedTCGAData

keep

If FALSE (default), remove the SummarizedExperiment objects that have been converted to RangedSummarizedExperiment

Details

Any SummarizedExperiment elements with gene symbols as rownames will have ranges added. Symbols where ranges can't be found are put in a new SummarizedExperiment.

Value

a MultiAssayExperiment where any of the original SummarizedExperiment containing gene symbols as rownames have been replaced or supplemented by a RangedSummarizedExperiment for miR that could be mapped to GRanges, and another SummarizedExperiment for miR that could not be mapped to GRanges.

Author(s)

L. Waldron

See Also

mirToRanges

Examples

library(MultiAssayExperiment)

data(miniACC)

symbolsToRanges(miniACC)


[Package TCGAutils version 1.2.2 Index]