Guitar (version 1.10.0)

makeGuitarCoordsFromGRangesList: makeGuitarCoordsFromGRangesList

Description

make Guitar Coordinates From a GRangesList object

Usage

makeGuitarCoordsFromGRangesList(comp, noBins = 100, collapseGene = FALSE, width = 51)

Arguments

comp

A GRangesList object

noBins

The number of sections the "transcript" of the GRangesList object will be equally divided into. This is the resolution of the Guitar coordinates. The larger noBins is, the clearer the visualization will be; however, more computation time and memory resource will be required. You may want to set a smaller number when using a slow computer. Default: 100.

collapseGene

Whether merge the Guitar coordinates from different transcripts. Default: FALSE.

width

The width of each check points. Default: 51

Value

Guitar coordinates will be generated, which provides a fast reference between genomic coordinates and the transcriptomic coordinates. By default, the returned value should be in GRanges format; if collapseGene = TRUE, GRangesList object will be returned.

Examples

gr1 <-  GRanges(seqnames = "chr2", ranges = IRanges(3000, 6000),
          strand = "+", score = 5L, GC = 0.45)
gr2 <-  GRanges(seqnames = c("chr1", "chr1"),
          ranges = IRanges(c(7000,13000), width = 3),
          strand = c("+"), score = 3:4, GC = c(0.3, 0.5))
grl <- GRangesList("gr1" = gr1, "gr2" = gr2)
tc <- makeGuitarCoordsFromGRangesList(grl, noBins = 5)
tc
mcols(tc)