ChIPpeakAnno: TSS at - strand
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Julie Zhu ★ 4.3k
@julie-zhu-3596
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Dear Guangchuang, Thank you very much for the feedback! Any feedbacks and responses sent to bioconductor@r-project.org are archived and web searchable. I would appreciate if you could send email to Bioconductor list for feedbacks forward. If you type ?annotatePeakInBatch, you will notice that FeatureLocForDistance is set to TSS by default, meaning that using start of feature when feature is on plus strand and using end of feature when feature is on minus strand. I think this is consistent with your expectation. The discrepancy described by you is due to the different annotation source used. You used transcript coordinates instead of gene coordinates stored in TSS.human.NCBI36. Another difference is that you used end(peak) to calculate distance while annotatePeakInBatch uses start(peak) by default. As a user, you can set PeakLocForDistance as start, end or middle of the peak. However, the result will be different. Please type ?annotatePeakInBatch to get the details to customize your parameter setting to fit your needs. Also annotation from different databases of different versions will be slightly different as you already pointed out. You can use getAnnotation function in ChIPpeakAnno to obtain the most recent Ensemble annotation. Alternatively, you could download annotation from UCSC genome browser and convert it to RangedData as annotation source. You also can download transcript coordinates to feed into annotatePeakInBatch to get the nearest transcript instead of gene. To test whether there exists this bug in the annotatePeakInBatch , let us use your example with a simple annotation consisting only two genes with the exact coordinates provided by you instead of using the built-in annotation. Looks like you are interested in peak end to TSS, so I will set PeakLocForDistance = "end" here. You can see that the results obtained, by customizing the parameters in annoatePeakInBatch, is consistent with what you get. require(ChIPpeakAnno) packageVersion("ChIPpeakAnno") peak <- RangedData(space="chr1", IRanges(24736757, 24737528)) TSS <- RangedData(space="chr1", IRanges(start=c(24742284 ,24683489,24683489,24683489,24695211), end = c( 24799466, 24700300,24740262, 24741587,24718169), names=c("NIPAL3", "STPG1-1","STPG1-2","STPG1-3","STPG1-4")), strand=c("+","-", "-", "-","-")) TSS RangedData with 5 rows and 1 value column across 1 space space ranges | strand <factor> <iranges> | <character> NIPAL3 chr1 [24742284, 24799466] | + STPG1-1 chr1 [24683489, 24700300] | - STPG1-2 chr1 [24683489, 24740262] | - STPG1-3 chr1 [24683489, 24741587] | - STPG1-4 chr1 [24695211, 24718169] | - ap <- annotatePeakInBatch(peak, Annotation=TSS, PeakLocForDistance="end") ap RangedData with 1 row and 9 value columns across 1 space space ranges | peak strand feature start_position end_position insideFeature distancetoFeature shortestDistance <factor> <iranges> | <character> <character> <character> <numeric> <numeric> <character> <numeric> <numeric> 1 STPG1-2 chr1 [24736757, 24737528] | 1 - STPG1-2 24683489 24740262 inside 2734 2734 fromOverlappingOrNearest <character> 1 STPG1-2 NearestStart Hope this clears things for you. Please do not hesitate to send feedbacks to Bioconductor list if you have additional questions or suggestions. Many thanks for the detailed examples! Best regards, Julie On 1/14/14 4:01 AM, "Yu, Guangchuang" <gcyu@connect.hku.hk> wrote: Dear Dr. Zhu, I found a bug of your package, please refer to http://ygc.name/2014/01/14/r-package-chippeakanno-sucks/ for details. Hope that it will solve in next release. Best Regards, Guangchuang I used R package ChIPpeakAnno for annotating peaks, and found that it handle the DNA strand in the wrong way. Maybe the developers were from the computer science but not biology background. ? > require(ChIPpeakAnno) > packageVersion("ChIPpeakAnno") [1] '2.10.0' > peak <- RangedData(space="chr1", IRanges(24736757, 24737528)) > data(TSS.human.GRCh37) > ap <- annotatePeakInBatch(peak, Annotation=TSS.human.GRCh37) > ap RangedData with 1 row and 9 value columns across 1 space space ranges | peak strand <factor> <iranges> | <character> <character> 1 ENSG00000001461 1 [24736757, 24737528] | 1 + feature start_position end_position insideFeature <character> <numeric> <numeric> <character> 1 ENSG00000001461 ENSG00000001461 24742284 24799466 upstream distancetoFeature shortestDistance fromOverlappingOrNearest <numeric> <numeric> <character> 1 ENSG00000001461 -5527 4756 NearestStart In this example, I defined a peak ranging from chr1:24736757 to chr1:24737528 and annotated the peak using ChIPpeakAnno package. It returns that the nearest gene is ENSG00000001461, whose gene symbol is NIPAL3. ? 5 > require(org.Hs.eg.db) > gene.ChIPpeakAnno <- select(org.Hs.eg.db, key=ap$feature, keytype="ENSEMBL", columns=c("ENSEMBL", "ENTREZID", "SYMBOL")) > gene.ChIPpeakAnno ENSEMBL ENTREZID SYMBOL 1 ENSG00000001461 57185 NIPAL3 When looking at the peak in Genome Browser, I found the nearest gene is STPG1. Screenshot 2014-01-13 22.00.46 The gene symbol, STPG1, was converted to ENTREZID for future processing. ?View Code RSPLUS 1 2 3 4 > gene.nearest <- select(org.Hs.eg.db, key="STPG1", keytype="SYMBOL", columns=c("ENSEMBL", "ENTREZID", "SYMBOL")) > gene.nearest SYMBOL ENSEMBL ENTREZID 1 STPG1 ENSG00000001460 90529 We can query the coordination of these two genes, and compare their distances to the peak. ?View Code RSPLUS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 > require(TxDb.Hsapiens.UCSC.hg19.knownGene) > knownGene <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene") > > gene.ChIPpeakAnno.info <- knownGene[[gene.ChIPpeakAnno$ENTREZID]] > gene.ChIPpeakAnno.info GRanges with 4 ranges and 2 metadata columns: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chr1 [24742245, 24781314] + | 618 uc010oek.2 [2] chr1 [24742245, 24799473] + | 619 uc001bjh.3 [3] chr1 [24742245, 24799473] + | 620 uc009vrc.3 [4] chr1 [24782628, 24792864] + | 621 uc001bji.3 --- seqlengths: chr1 chr2 ... chrUn_gl000249 249250621 243199373 ... 38502 After getting the information of the gene annotated by ChIPpeakAnno, I also found that the ranges of the gene is slightly different from the one returned by annotatePeakInBatch function. This may due to the variation of different versions and it's not a big deal. As the gene, NIPAL3, is encoded in + strand, the nearest distance is: ?View Code RSPLUS 1 2 > min(abs(start(peak) - startgene.ChIPpeakAnno.info))) [1] 5488 While the gene, STPG1, is encoded in - strand, the end of the gene coordination is actually the start position of the gene and the start of the gene coordination is the end position. So the distance should be calculated by the end coordination. [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
@julie-zhu-3596
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