SummarizedExperiment_tidiers {biobroom} | R Documentation |
Tidying methods for Biobase's SummarizedExperiment objects
## S3 method for class 'RangedSummarizedExperiment' tidy(x, addPheno = FALSE, assay = SummarizedExperiment::assayNames(x)[1L], ...)
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 |
... |
extra arguments (not used) |
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.
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.
if (require("SummarizedExperiment", "airway")) { data(airway) se <- airway tidy(se) }