SummarizedExperiment_tidiers

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Tidying methods for Biobase's SummarizedExperiment objects

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)
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.

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.

Aliases
  • SummarizedExperiment_tidiers
  • tidy.RangedSummarizedExperiment
Examples
if (require("SummarizedExperiment", "airway")) {
    data(airway)

    se <- airway
    tidy(se)
}

Documentation reproduced from package biobroom, version 1.4.2, License: LGPL

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