Argument Description
object A profileplyr object
species GREAT accepts “hg19”, “mm10”, “mm9”, “danRer7” (zebrafish)
… pass to ‘submitGreatJob’ function from the rGreat package

Example

The GREAT algorithm for annotating genomic ranges with genes in the same regulatory region is also commonly used. profileplyr has a function, annotateRanges_great(), which will add a column to the range metadata showing whether that range is in the regulatory region of a particular gene. Note this is different from ChIPseeker, which will annotate with the closest gene. annotateRagnes_great() may also result in duplication of ranges within the profileplyr object if a range is in the regulatory region of two or more genes.
proplyr_object_subset <- annotateRanges_great(proplyr_object_subset,
                                                   species = "hg19")

rowRanges(proplyr_object_subset)[1:3]
## GRanges object with 3 ranges and 7 metadata columns:
##           seqnames          ranges strand |        name     score
##              <Rle>       <IRanges>  <Rle> | <character> <numeric>
##   giID808     chr1 1250419-1251035      + |        <NA>         0
##   giID808     chr1 1250419-1251035      + |        <NA>         0
##   giID785     chr1 2209362-2211662      + |        <NA>         0
##                          sgGroup     giID    names      SYMBOL
##                         <factor> <factor> <factor> <character>
##   giID808 K27ac_top10_HUES64.bed  giID808     <NA>       PUSL1
##   giID808 K27ac_top10_HUES64.bed  giID808     <NA>      CPSF3L
##   giID785 K27ac_top10_HUES64.bed  giID785     <NA>        RER1
##           distanceToTSS
##               <numeric>
##   giID808          6780
##   giID808          9262
##   giID785       -112760
##   -------
##   seqinfo: 24 sequences from an unspecified genome; no seqlengths
The ‘SYMBOL’ column of this object contains the gene annotation for that region, and importantly this can be used with the ‘groupBy’ function within profileplyr to group the ranges by gene sets.