Convert GFF format to RangedData

Description

Convert GFF format to RangedData. This function will be depreciated. Use function toGRanges instead.

Usage

GFF2RangedData(data.GFF,header=FALSE, ...)

Arguments

Value

RangedData with slot start holding the start position of the feature, slot end holding the end position of the feature, slot names holding the id of the feature, slot space holding the chromosome location where the feature is located. In addition, the following variables are included.

Note

For converting the peakList in GFF format to RangedData before calling annotatePeakInBatch function

Author(s)

Lihua Julie Zhu

Examples

  test.GFF = data.frame(cbind(seqname  = c("chr1", "chr2"), 
  source=rep("Macs", 2), 
  feature=rep("peak", 2), 
  start=c("100", "1000"), 
  end=c("200", "1100"), 
  score=c(60, 26), 
  strand=c(1, -1), 
  frame=c(".", 2), 
  group=c("peak1", "peak2")))
  test.rangedData = GFF2RangedData(test.GFF)

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(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/GFF2RangedData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GFF2RangedData
> ### Title: Convert GFF format to RangedData
> ### Aliases: GFF2RangedData GFF2RangedData-deprecated
> ### Keywords: misc
> 
> ### ** Examples
> 
>   test.GFF = data.frame(cbind(seqname  = c("chr1", "chr2"), 
+   source=rep("Macs", 2), 
+   feature=rep("peak", 2), 
+   start=c("100", "1000"), 
+   end=c("200", "1100"), 
+   score=c(60, 26), 
+   strand=c(1, -1), 
+   frame=c(".", 2), 
+   group=c("peak1", "peak2")))
>   test.rangedData = GFF2RangedData(test.GFF)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>