geneRanges: Gene Ranges

Description Usage Arguments

Description

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

Usage

1
geneRanges(chrom, tss, strand, proxUp, proxDown, distal, n = length(chrom))

Arguments

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)


alexjgriffith/CCCA documentation built on May 10, 2019, 8:52 a.m.