makeGuitarCoordsFromGRangesList {Guitar} | R Documentation

## 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.

### Author(s)

Jia Meng <jia.meng@hotmail.com>

### 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)

[Package Guitar version 1.18.0 Index]