Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/promoterRegions.R
Create a SAF data-frame of genewise promoter regions.
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promoterRegions( annotation = "mm10", upstream = 3000L, downstream = 2000L)
a data.frame containing gene annotation in SAF format or a character string giving the name of a genome with built-in annotation. If using built-in annotation, the character string should be one of the following:
an integer giving the number of upstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately upstream (5' end) from transcriptional start site of each gene.
an integer giving the number of downstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately downstream (3' end) from transcriptional start site of each gene.
This function takes as input a SAF format gene annotation and produces a SAF format data.frame containing the chromosomal coordinates of the specified promoter region for each gene.
featureCounts for definition of the SAF format.
Regardless of the
downstream values, the downstream end of the region never extends past the end of the gene and the upstream end never extends outside the relevant chromosome.
downstream to an infinite or large value will cause the body of each gene to be included.
A SAF format
data.frame with columns
Gordon K Smyth
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# To get whole gene bodies for the mouse genome: x <- promoterRegions("mm10", upstream = 0, downstream = Inf) head(x)
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