makeGuitarCoordsFromGRangesList

Description

make Guitar Coordinates From a GRangesList object

Usage

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

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Guitar)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: rtracklayer
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: ggplot2
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Guitar/makeGuitarCoordsFromGRangesList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeGuitarCoordsFromGRangesList
> ### Title: makeGuitarCoordsFromGRangesList
> ### Aliases: makeGuitarCoordsFromGRangesList
> ### Keywords: Guitar GRanges GRangesList
> 
> ### ** 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
GRanges object with 10 ranges and 3 metadata columns:
      seqnames         ranges strand |     txid       pos  interval
         <Rle>      <IRanges>  <Rle> | <factor> <numeric> <numeric>
  gr1     chr2 [ 3275,  3325]      + |      gr1       0.1     600.2
  gr2     chr1 [ 6975,  7025]      + |      gr2       0.1       1.2
  gr1     chr2 [ 3875,  3925]      + |      gr1       0.3     600.2
  gr2     chr1 [ 6976,  7026]      + |      gr2       0.3       1.2
  gr1     chr2 [ 4475,  4525]      + |      gr1       0.5     600.2
  gr2     chr1 [ 6977,  7027]      + |      gr2       0.5       1.2
  gr1     chr2 [ 5075,  5125]      + |      gr1       0.7     600.2
  gr2     chr1 [12976, 13026]      + |      gr2       0.7       1.2
  gr1     chr2 [ 5675,  5725]      + |      gr1       0.9     600.2
  gr2     chr1 [12977, 13027]      + |      gr2       0.9       1.2
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> mcols(tc)
DataFrame with 10 rows and 3 columns
       txid       pos  interval
   <factor> <numeric> <numeric>
1       gr1       0.1     600.2
2       gr2       0.1       1.2
3       gr1       0.3     600.2
4       gr2       0.3       1.2
5       gr1       0.5     600.2
6       gr2       0.5       1.2
7       gr1       0.7     600.2
8       gr2       0.7       1.2
9       gr1       0.9     600.2
10      gr2       0.9       1.2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>