narrowPeaktoGRanges

Description

read the narrowpeak format from MACS software into GRangesList object.

NAME_peaks.narrowPeak is BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser. Definition of some specific columns are: 5th: integer score for display 7th: fold-change 8th: -log10pvalue 9th: -log10qvalue 10th: relative summit position to peak start.

Usage

narrowPeaktoGRanges(file)

Arguments

Value

A GRanges object will be returned.

References

MACS2 software: https://github.com/taoliu/MACS/tree/master/MACS2

Examples

narrowPeak=system.file("extdata", "m6A_hg19_1000peaks_macs2.narrowPeak", package="Guitar")
m6A_Bcell <- narrowPeaktoGRanges(narrowPeak) # bam imported as GAlignments
m6A_Bcell

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/narrowPeaktoGRanges.Rd_%03d_medium.png", width=480, height=480)
> ### Name: narrowPeaktoGRanges
> ### Title: narrowPeaktoGRanges
> ### Aliases: narrowPeaktoGRanges
> 
> ### ** Examples
> 
> narrowPeak=system.file("extdata", "m6A_hg19_1000peaks_macs2.narrowPeak", package="Guitar")
> m6A_Bcell <- narrowPeaktoGRanges(narrowPeak) # bam imported as GAlignments
> m6A_Bcell
GRanges object with 1000 ranges and 10 metadata columns:
         seqnames               ranges strand |       V1        V2        V3
            <Rle>            <IRanges>  <Rle> | <factor> <integer> <integer>
     [1]     chr1       [14409, 14906]      * |     chr1     14409     14906
     [2]     chr1       [15315, 15532]      * |     chr1     15315     15532
     [3]     chr1       [16663, 16787]      * |     chr1     16663     16787
     [4]     chr1       [16964, 17085]      * |     chr1     16964     17085
     [5]     chr1       [17676, 17798]      * |     chr1     17676     17798
     ...      ...                  ...    ... .      ...       ...       ...
   [996]     chr1 [38155955, 38156121]      * |     chr1  38155955  38156121
   [997]     chr1 [38172672, 38172772]      * |     chr1  38172672  38172772
   [998]     chr1 [38173969, 38174361]      * |     chr1  38173969  38174361
   [999]     chr1 [38174536, 38174636]      * |     chr1  38174536  38174636
  [1000]     chr1 [38259802, 38260396]      * |     chr1  38259802  38260396
                                        V4        V5       V6        V7
                                  <factor> <integer> <factor> <numeric>
     [1]    cellular_dox_macs_kpdup_peak_1      1511        .  12.26350
     [2]    cellular_dox_macs_kpdup_peak_2        84        .   4.52297
     [3]    cellular_dox_macs_kpdup_peak_3       242        .   4.05520
     [4]    cellular_dox_macs_kpdup_peak_4        20        .   1.66964
     [5]    cellular_dox_macs_kpdup_peak_5       103        .   2.23147
     ...                               ...       ...      ...       ...
   [996]  cellular_dox_macs_kpdup_peak_996        35        .   4.04413
   [997]  cellular_dox_macs_kpdup_peak_997       197        .   7.80644
   [998]  cellular_dox_macs_kpdup_peak_998       291        .  11.82129
   [999]  cellular_dox_macs_kpdup_peak_999        38        .   3.68638
  [1000] cellular_dox_macs_kpdup_peak_1000       120        .   6.33227
                V8        V9       V10
         <numeric> <numeric> <integer>
     [1] 155.56317 151.18591        96
     [2]  11.31053   8.40897        57
     [3]  27.62019  24.28956        49
     [4]   4.54747   2.03608         1
     [5]  13.36805  10.39292        27
     ...       ...       ...       ...
   [996]   6.19355   3.53633       133
   [997]  23.01747  19.77756        49
   [998]  32.53416  29.11507        99
   [999]   6.54282   3.87012        21
  [1000]  15.10463  12.07185       158
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>