ChIP peak annotation: how to get all genes that overlap each peak?
0
0
Entering edit mode
94133 • 0
@94133-14305
Last seen 4.5 years ago
USA, Stanford

How do I get all genes that overlap a peak as a comma separated column within a single row for the peak?

I tried ChIPseeker:

annotatePeak(peaks, level = "gene", 
                         addFlankGeneInfo = FALSE,
                         assignGenomicAnnotation = TRUE,
                         TxDb = TxDb.Mmusculus.UCSC.mm10.knownGene, 
                         annoDb = "org.Mm.eg.db",
                         ignoreOverlap = FALSE,
                         overlap="all")

Result: 

Doesn't report all genes within peak. If change addFlankGeneInfo = TRUE, get some of the genes but doesn't cover exact peak size so not useful in this case.

 

I tried ChIPpeakAnno:

ucsc.mm10.knownGene <- genes(TxDb.Mmusculus.UCSC.mm10.knownGene)
gr_peaks <- toGRanges(merge_peaks, format="BED", header = FALSE, feature = "gene")
peaks_anno <- annotatePeakInBatch(gr_peaks, 
                                        AnnotationData = ucsc.mm10.knownGene,
                                        output = "both",
                                        select = "all")
peaks_anno <- addGeneIDs(annotatedPeak = peaks_anno,
                              orgAnn = "org.Mm.eg.db",
                              feature_id_type = "entrez_id",
                              IDs2Add = "symbol")

Result:

Returns all genes in peaks but in new rows instead of list in one column.

seqnames start end width strand feature start_position end_position feature_strand insideFeature distancetoFeature shortestDistance fromOverlappingOrNearest symbol

X07696.103889 chr11 96268247 96356723 88477 X07696 103889 96351632 96354014 + includeFeature -83385 2709 NearestLocation Hoxb2

X07696.15410 chr11 96268247 96356723 88477 X07696 15410 96323126 96347930 + includeFeature -54879 8793 NearestLocation Hoxb3

X07696.15412 chr11 96268247 96356723 88477 X07696 15412 96318267 96321638 + includeFeature -50020 35085 NearestLocation Hoxb4

X07696.15413 chr11 96268247 96356723 88477 X07696 15413 96303512 96306121 + includeFeature -35265 35265 NearestLocation Hoxb5

X07696.15414 chr11 96268247 96356723 88477 X07696 15414 96299171 96301569 + includeFeature -30924 30924 NearestLocation Hoxb6

X07696.15415 chr11 96268247 96356723 88477 X07696 15415 96286646 96290163 + includeFeature -18399 18399 NearestLocation Hoxb7

X07696.15416 chr11 96268247 96356723 88477 X07696 15416 96281905 96285325 + includeFeature -13658 13658 NearestLocation Hoxb8

X07696.15417 chr11 96268247 96356723 88477 X07696 15417 96271330 96276593 + includeFeature -3083 3083 NearestLocation Hoxb9

 

Want something like:

seqnames start end width strand feature start_position end_position feature_strand insideFeature distancetoFeature shortestDistance fromOverlappingOrNearest symbol

X07696.103889 chr11 96268247 96356723 88477 X07696 103889 96351632 96354014 + includeFeature -83385 2709 NearestLocation Hoxb2, Hoxb3, Hoxb4, Hoxb5, Hoxb6, Hoxb7, Hoxb8, Hoxb9

 

ChIP-seq chippeakanno chipseeker • 1.9k views
ADD COMMENT
1
Entering edit mode

Did you tried ?condenseMatrixByColnames

for example:

library(ChIPpeakAnno)

res <- condenseMatrixByColnames(as.matrix(peaks_anno), "peak")

 

ADD REPLY
0
Entering edit mode

Thanks for your reply!

I tried that but get:

Error in as.vector(x) : no method for coercing this S4 class to a vector

Suggestions?

I made workaround with dplyr, but have to convert from class "GRanges" to "data.frame" to do that.

 

 

 

ADD REPLY
1
Entering edit mode

try this:

res <- condenseMatrixByColnames(as.matrix(as.data.frame(peaks_anno)), "peak")

ADD REPLY
0
Entering edit mode

Thanks! Is there a way to keep res as "GRanges" object?

 

ADD REPLY
1
Entering edit mode

NO. after merging, you can create a GRanges object by the new dataset.

ADD REPLY
0
Entering edit mode

Great, thanks for your quick reply!

ADD REPLY

Login before adding your answer.

Traffic: 816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6