Hello,

I should preface this with the general, "I'm new and don't know what I'm doing, but I'm trying to learn" message.  I've just started to learn R (using 3.4) and am trying to use ChIPPeakAnno to 1) annotate my peaks 2) compare 3 datasets for TSS, TSS+200bp, etc.  

Using the following script: 

library(biomaRt)
library(org.Mm.eg.db)
mart <- useMart("ensembl", "mmusculus_gene_ensembl")
AnnotationData <- getAnnotation(mart, featureType="TSS")
data("TSS.mouse.NCBIM37")

d3.k4m1 <- import.bed("d3_TCR_k4m1_summits.bed")
d3.k4m1.RD <- RangedData(d3.k4m1)
d3.k4m1.TGR <- toGRanges(d3.k4m1.RD)

I get this error and am unable to procede with anything:

> d3.k4m1.anno <- annotatePeakInBatch(d3.k4m1.TGR, mart, featureType="TSS", AnnotationData = TSS.mouse.NCBIM37, output = "both", mutliple=FALSE, maxgap = 0L, PeakLocForDistance = "middle", FeatureLocForDistance = "TSS", select="all", ignore.strand = FALSE, bindingRegion = NULL)
There were 37 warnings (use warnings() to see them)
> d3.k4m1.fullanno <- addGeneIDs(d3.k4m1.TGR, mart=mart, feature_id_type="ensembl_gene_id", IDs2Add= c("ensembl_gene_id","description", "chromosome_name", "start_position", "end_position", "external_gene_name", "go_id", "name_1006"), silence=TRUE)
Error: There is no feature column in annotatedPeak or 
             annotatedPeak has size 0!
In addition: Warning message:
In is.na(feature_ids) :
  is.na() applied to non-(list or vector) of type 'NULL'

This error is on a dataset with 57,000 peaks but when I use a dataset with only 5000 peaks or so, I have no problems so I get that the file size is maybe an issue but I'm unsure how to fix it.  I would appreciate any assistance.  

Many thanks.

Hi,

Please have a try of following code, and let me know if there is any question.

 
library(ChIPpeakAnno)
library(biomaRt) 
library(org.Mm.eg.db) 
mart <- useMart("ensembl", "mmusculus_gene_ensembl")
# you can get annotationData from TxDb
#library(TxDb.Mmusculus.UCSC.mm10.knownGene) 
#AnnotationData <- toGRanges(TxDb.Mmusculus.UCSC.mm10.knownGene) ## if you use TxDb, parameters feature_id_type of addGeneIDs should be changed.
# or EnsDb
#library(EnsDb.Mmusculus.v79)
#AnnotationData <- toGRanges(EnsDb.Mmusculus.v79) 
data("TSS.mouse.NCBIM37")
AnnotationData <- TSS.mouse.NCBIM37
d3.k4m1 <- toGRanges("d3_TCR_k4m1_summits.bed", format="BED") #import to GRanges
d3.k4m1.anno <- annotatePeakInBatch(d3.k4m1, featureType="TSS", AnnotationData = AnnotationData, output = "both", mutliple=FALSE, maxgap = 0L, PeakLocForDistance = "middle", FeatureLocForDistance = "TSS", select="all", ignore.strand = FALSE, bindingRegion = NULL)

head(d3.k4m1.anno) # take a look about the annotations

d3.k4m1.fullanno <- addGeneIDs(d3.k4m1.anno, mart=mart, feature_id_type="ensembl_gene_id", IDs2Add= c("ensembl_gene_id","description", "external_gene_name", "go_id", "name_1006"), silence=TRUE)

addGeneIDs is used to add annotations for the output of annotatePeakInBatch.

Thanks!  I saw that I had an error in that I was trying to use both mart and data arguments at the same time.  An accident of playing around with various parameters.  Many thanks for your help!