promoterRegions {Rsubread} | R Documentation |
Create an SAF data-frame of genewise promoter regions.
promoterRegions( annotation = "mm10", upstream = 3000L, downstream = 2000L)
annotation |
a character string giving the name of a genome with built-in annotation or an SAF format gene annotation. If using built-in annotation, the character string should be one of the following: |
upstream |
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. |
downstream |
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 an SAF format gene annotation and produces an SAF format annotation that contains chromosomal coordinates of promoter region of each gene.
See featureCounts
for definition of the SAF format.
Built-in annotations can be accessed via function getInBuiltAnnotation
.
An SAF format data.frame
with columns GeneID
, Chr
, Start
, End
and Strand
.
Gordon K Smyth
featureCounts
, getInBuiltAnnotation
x <- promoterRegions() head(x)