Implements the two step Stanford GREAT genomic region generation. First each gene is assigned a basal region defined as the TSS +/- the proxUp and proxDown value (dependent on strand). Second each Gene has its effective region expaned up to the lower of a distal maximum and the basal limits of other genes. The returned values are in the order of the input chrom tss strand variables. note: the indicies of the chrom tss and strand parameters should all relate to the same gene, ie a chrom[100] tss[100] and strand[100] should all be infromation from the same gene
1 | geneRanges(chrom, tss, strand, proxUp, proxDown, distal, n = length(chrom))
|
chrom |
A list of chromosomes, one for each gene |
tss |
The list of gene TSS |
strand |
The stream directions of each of the genes |
proxUp |
Upstream basal extension (independent of other genes) |
proxDown |
Downstream basal extension (independent of other genes) |
distal |
The limit of gene extension (in either direction) |
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