Description Usage Arguments Details Value Examples
Determines what genes directly under peaks are actually unique between two different upstream extension levels.
1 |
organism |
Object name assigned from readGFF() command. |
start |
Lower bound of upstream extension. |
end |
Upper bound of upstream extension. |
V1-V3 denote the chromosome/start/end positions of the peaks, V4-V6 denote the respective values of the genes, V7 is the gene ID (e.g., Ensembl ID), V8 is the gene name, and V9 is the distance of peak to nearest gene.
A data.table of unique genes located under peaks between two upstream extension levels.
1 2 3 4 5 | library(rtracklayer)
rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
peaksInput(fpath)
distinct(rat, 2000, 3000)
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