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Last data update: 2014.03.03

R: Add metadata of the GRanges objects used for...

addMetadata

R Documentation

Add metadata of the GRanges objects used for findOverlapsOfPeaks

Description

Add metadata to to overlapping peaks after calling findOverlapsOfPeaks.

Usage

addMetadata(ol, colNames=NULL, FUN=c, ...)

Arguments

`ol`	An object of overlappingPeaks, which is output of findOverlapsOfPeaks.
`colNames`	Names of metadata column to be added. If it is NULL, addMetadata will guess what to add.
`FUN`	A function to be called
`...`	Arguments to the function call.

Value

return value is An object of overlappingPeaks.

Author(s)

Jianhong Ou

Examples

peaks1 <- GRanges(seqnames=c(6,6,6,6,5),
                 IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
                         end=c(1555199,1560599,1565199,1573799,167893599),
                         names=c("p1","p2","p3","p4","p5")),
                 strand="+",
                 score=1:5, id=letters[1:5])
peaks2 <- GRanges(seqnames=c(6,6,6,6,5),
                  IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
                          end=c(1550599,1560799,1565399,1571199,167888999),
                          names=c("f1","f2","f3","f4","f5")),
                  strand="+",
                  score=6:10, id=LETTERS[1:5])
ol <- findOverlapsOfPeaks(peaks1, peaks2)
addMetadata(ol)

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(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/addMetadata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addMetadata
> ### Title: Add metadata of the GRanges objects used for findOverlapsOfPeaks
> ### Aliases: addMetadata
> ### Keywords: misc
> 
> ### ** Examples
> 
> peaks1 <- GRanges(seqnames=c(6,6,6,6,5),
+                  IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
+                          end=c(1555199,1560599,1565199,1573799,167893599),
+                          names=c("p1","p2","p3","p4","p5")),
+                  strand="+",
+                  score=1:5, id=letters[1:5])
> peaks2 <- GRanges(seqnames=c(6,6,6,6,5),
+                   IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
+                           end=c(1550599,1560799,1565399,1571199,167888999),
+                           names=c("f1","f2","f3","f4","f5")),
+                   strand="+",
+                   score=6:10, id=LETTERS[1:5])
> ol <- findOverlapsOfPeaks(peaks1, peaks2)
> addMetadata(ol)
$venn_cnt
     peaks1 peaks2 Counts
[1,]      0      0      0
[2,]      0      1      1
[3,]      1      0      1
[4,]      1      1      4
attr(,"class")
[1] "VennCounts"

$peaklist
$peaklist$peaks2
GRanges object with 1 range and 3 metadata columns:
      seqnames                 ranges strand |       peakNames          id
         <Rle>              <IRanges>  <Rle> | <CharacterList> <character>
  [1]        5 [167888600, 167888999]      + |      peaks2__f5           E
            score
      <character>
  [1]          10
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

$peaklist$peaks1
GRanges object with 1 range and 3 metadata columns:
      seqnames                 ranges strand |       peakNames          id
         <Rle>              <IRanges>  <Rle> | <CharacterList> <character>
  [1]        5 [167889600, 167893599]      + |      peaks1__p5           e
            score
      <character>
  [1]           5
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

$peaklist$`peaks1///peaks2`
GRanges object with 3 ranges and 3 metadata columns:
      seqnames             ranges strand |                            peakNames
         <Rle>          <IRanges>  <Rle> |                      <CharacterList>
  [1]        6 [1543200, 1560799]      + | peaks1__p1,peaks2__f1,peaks2__f2,...
  [2]        6 [1563000, 1565399]      + |                peaks1__p3,peaks2__f3
  [3]        6 [1569400, 1573799]      + |                peaks2__f4,peaks1__p4
            id    score
        <list>   <list>
  [1] ######## ########
  [2] ######## ########
  [3] ######## ########
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths


$overlappingPeaks
$overlappingPeaks$`peaks1///peaks2`
                          peaks1 seqnames   start     end width strand
peaks1__p1_peaks2__f1 peaks1__p1        6 1543200 1555199 12000      +
peaks1__p1_peaks2__f2 peaks1__p1        6 1543200 1555199 12000      +
peaks1__p2_peaks2__f2 peaks1__p2        6 1557200 1560599  3400      +
peaks1__p3_peaks2__f3 peaks1__p3        6 1563000 1565199  2200      +
peaks1__p4_peaks2__f4 peaks1__p4        6 1569800 1573799  4000      +
                          peaks2 seqnames   start     end width strand
peaks1__p1_peaks2__f1 peaks2__f1        6 1549800 1550599   800      +
peaks1__p1_peaks2__f2 peaks2__f2        6 1554400 1560799  6400      +
peaks1__p2_peaks2__f2 peaks2__f2        6 1554400 1560799  6400      +
peaks1__p3_peaks2__f3 peaks2__f3        6 1565000 1565399   400      +
peaks1__p4_peaks2__f4 peaks2__f4        6 1569400 1571199  1800      +
                      overlapFeature shortestDistance
peaks1__p1_peaks2__f1 includeFeature             4600
peaks1__p1_peaks2__f2   overlapStart              799
peaks1__p2_peaks2__f2         inside              200
peaks1__p3_peaks2__f3   overlapStart              199
peaks1__p4_peaks2__f4     overlapEnd              400


$all.peaks
$all.peaks[[1]]
GRanges object with 5 ranges and 2 metadata columns:
             seqnames                 ranges strand |     score          id
                <Rle>              <IRanges>  <Rle> | <integer> <character>
  peaks1__p1        6 [  1543200,   1555199]      + |         1           a
  peaks1__p2        6 [  1557200,   1560599]      + |         2           b
  peaks1__p3        6 [  1563000,   1565199]      + |         3           c
  peaks1__p4        6 [  1569800,   1573799]      + |         4           d
  peaks1__p5        5 [167889600, 167893599]      + |         5           e
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

$all.peaks[[2]]
GRanges object with 5 ranges and 2 metadata columns:
             seqnames                 ranges strand |     score          id
                <Rle>              <IRanges>  <Rle> | <integer> <character>
  peaks2__f1        6 [  1549800,   1550599]      + |         6           A
  peaks2__f2        6 [  1554400,   1560799]      + |         7           B
  peaks2__f3        6 [  1565000,   1565399]      + |         8           C
  peaks2__f4        6 [  1569400,   1571199]      + |         9           D
  peaks2__f5        5 [167888600, 167888999]      + |        10           E
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths


attr(,"class")
[1] "overlappingPeaks"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>