Description

SummarizedExperiment container

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information related to the experiment as a whole
e.g. [ id:'SRP123456' ]

matrix_files (directory)

One or more paths to CSV or TSV matrix files. All files must have the
same rows and columns.

*.{csv,tsv}

meta2 (map)

Groovy Map containing reference information related to the species
reference from which matrix rows are derived e.g. [ id:'yeast' ]

rowdata (file)

Metadata on matrix features. One column must contain all matrix row
IDs.

*.{csv,tsv}

meta3 (map)

Groovy Map containing information related to the experiment as a whole,
as represented by the matrix columns and the sample sheet e.g.
[id:'SRP123456' ]

coldata (file)

Metadata on matrix columns. One column must contain all matrix column
IDs.

*.{csv,tsv}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information related to the experiment as a whole
e.g. [ id:'SRP123456' ]

rds (file)

Serialised SummarizedExperiment object

*.SummarizedExperiment.rds

log (file)

dump of R SessionInfo

*.log

versions (file)

File containing software versions

versions.yml
included in
riboseq
maintainer
Github user pinin4fjords
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

summarizedexperiment
Artistic-2.0

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

bioconductor.org/packages/release/bioc/html/SummarizedExperiment bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment https://github.com/Bioconductor/SummarizedExperiment 10.18129/B9.bioc.SummarizedExperiment