grNew: Create a simple GRanges object.

In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Create a simple Granges object based on a sequence of exons on one strand of one chromosome. This could be a gene, a transcript, or one side of a fusion. Defaults to '*' if strand is not specified. Coordinates are given as if the exons were on the positive strand, in 1-based coordinates. This will be backawards from the actual sequence if the gene is on the negative strand. Ranges will be sorted by start and then by end.

Usage

grNew(start, end, chr, strand = "*")

Arguments

start	A vector giving the starting (lower) genomic coordinates of the exons. Must be specified.
end	A vector giving the ending (higher) genomic coordinates of the exons. Must be specified.
chr	The chromosome (singular) on which these exons occur, like 'chr1' or 'chrX'. Must be specified.
strand	The strand the exons are actually on, as '+', '-', or '*'. Defaults to '*' if not specified.

Value

The genomicRanges object built from the exons.

jefferys/fusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.