Four steps for peak annotation

The purpose of this quick start is to introduce the four newly implemented functions, toRanges, annoGO, annotatePeakInBatch, and addGeneIDs in the new version of the ChIPpeakAnno. With those wrapper functions, the annotation of ChIP-Seq peaks becomes streamlined into four major steps:

1 Read peak data with toGRanges 2 Generate annotation data with toGRanges 3 Annotate peaks with annotatePeakInBatch 4 Add additional information with addGeneIDs

Most of time user can use the default settings of the arguments of those functions. This makes the annotation pipeline straightforward and easy to use.

Note that the version of the annotation data must match with the genome used for mapping because the coordinates may differ for different genome releases. For example, if you are using Mus_musculus.v103 for mapping, you’d best also use EnsDb.Mmusculus.v103 for annotation. For more information about how to prepare the annotation data, please refer ?getAnnotation.

Use case 1: Four steps to annotate peak data with EnsDb

Step 1: Convert the peak data to GRanges with toGRanges

## First, load the ChIPpeakAnno package
library(ChIPpeakAnno)
path <- system.file("extdata", "Tead4.broadPeak", package="ChIPpeakAnno")
peaks <- toGRanges(path, format="broadPeak")
peaks[1:2]
## GRanges object with 2 ranges and 4 metadata columns:
##             seqnames        ranges strand |     score signalValue    pValue
##                <Rle>     <IRanges>  <Rle> | <integer>   <numeric> <numeric>
##   peak12338     chr2 175473-176697      * |       206      668.42        -1
##   peak12339     chr2 246412-246950      * |        31      100.23        -1
##                qValue
##             <numeric>
##   peak12338        -1
##   peak12339        -1
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

Step 2: Prepare annotation data with toGRanges

library(EnsDb.Hsapiens.v75)
annoData <- toGRanges(EnsDb.Hsapiens.v75)
annoData[1:2]
## GRanges object with 2 ranges and 1 metadata column:
##                   seqnames      ranges strand |   gene_name
##                      <Rle>   <IRanges>  <Rle> | <character>
##   ENSG00000223972     chr1 11869-14412      + |     DDX11L1
##   ENSG00000227232     chr1 14363-29806      - |      WASH7P
##   -------
##   seqinfo: 273 sequences (1 circular) from 2 genomes (hg19, GRCh37)

Step 3: Annotate the peaks with annotatePeakInBatch

## keep the seqnames in the same style if needed
seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
## do annotation by nearest TSS
anno <- annotatePeakInBatch(peaks, AnnotationData=annoData)
anno[1:2]
## GRanges object with 2 ranges and 13 metadata columns:
##                             seqnames        ranges strand |     score
##                                <Rle>     <IRanges>  <Rle> | <integer>
##   peak12338.ENSG00000227061     chr2 175473-176697      * |       206
##   peak12339.ENSG00000143727     chr2 246412-246950      * |        31
##                             signalValue    pValue    qValue        peak
##                               <numeric> <numeric> <numeric> <character>
##   peak12338.ENSG00000227061      668.42        -1        -1   peak12338
##   peak12339.ENSG00000143727      100.23        -1        -1   peak12339
##                                     feature start_position end_position
##                                 <character>      <integer>    <integer>
##   peak12338.ENSG00000227061 ENSG00000227061         197569       202605
##   peak12339.ENSG00000143727 ENSG00000143727         264140       278283
##                             feature_strand insideFeature distancetoFeature
##                                <character>   <character>         <numeric>
##   peak12338.ENSG00000227061              +      upstream            -22096
##   peak12339.ENSG00000143727              +      upstream            -17728
##                             shortestDistance fromOverlappingOrNearest
##                                    <integer>              <character>
##   peak12338.ENSG00000227061            20872          NearestLocation
##   peak12339.ENSG00000143727            17190          NearestLocation
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths
# A pie chart can be used to demonstrate the overlap features of the peaks.
pie1(table(anno$insideFeature))