Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/reproduce_ranges.R
This function reproduces the gene or exon level information used for creating
the RangedSummarizedExperiment-class
objects provided by recount. The annotation is based on
Gencode v25 with the gene-level
information extracted with genes()
(see
transcripts with default arguments.
1 | reproduce_ranges(level = "gene", db = "Gencode.v25")
|
level |
Either |
db |
Either |
For Gencode.v25, we use the comprehensive gene annotation (regions:
CHR
) from https://www.gencodegenes.org/releases/25.html
(GRCh38.p7).
Note that gene symbols have changed over time. This answer in the Bioconductor support forum details how to obtain the latest gene symbol mappings: https://support.bioconductor.org/p/126148/#126173.
Either a GRanges-class object like recount_genes or a GRangesList-class object like recount_exons.
Leonardo Collado-Torres
recount_genes, recount_exons, https://github.com/nellore, https://jhubiostatistics.shinyapps.io/recount/
1 2 3 4 5 6 7 8 9 | ## Not run:
## Reproduce gene level information
genes <- reproduce_ranges()
## Compare against recount_genes
length(genes)
length(recount_genes)
## End(Not run)
|
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