biobroom (version 1.4.2)

SummarizedExperiment_tidiers: Tidying methods for Biobase's SummarizedExperiment objects

Description

Tidying methods for Biobase's SummarizedExperiment objects

Usage

"tidy"(x, addPheno = FALSE, assay = SummarizedExperiment::assayNames(x)[1L], ...)

Arguments

x

SummarizedExperiment object

addPheno

whether columns should be included in the tidied output for those in the SummarizedExperiment colData

assay

Which assay to return as the value column. Defaults to assays(x)[[1L]]

...

extra arguments (not used)

Value

tidy returns a data frame with one row per gene-sample combination, with columns

gene

gene name

sample

sample name (from column names)

value

expressions

If addPheno is TRUE then information from colData is added.

Details

addPheno=TRUE adds columns that are redundant (since they add per-sample information to a per-sample-per-gene data frame), but that are useful for some kinds of graphs and analyses.

Examples

if (require("SummarizedExperiment", "airway")) {
    data(airway)

    se <- airway
    tidy(se)
}

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