[BioC] ChIPpeakAnno 2.12.2 bug

Tue Aug 19 20:25:56 CEST 2014

Dear Matt,

Thank you again for the report. The bug has been fixed in version 2.12.3.
You can check out the new version by svn,

svn checkout 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks
/ChIPpeakAnno/@93472 path/to/save/ChIPpeakAnno.2.12.3

Please let me know if you have any issues.

Yours Sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605

On 8/18/14 2:49 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at fs.fed.us> wrote:

>Hi
>
>Thanks for working on this but I am still getting the same result even
>with 2.13.1. The annotatePeakInBatch is not assigning peaks to features
>correctly when genes are located on the negative strand. Below is an
>example that produces an incorrect result when using annotatePeakInBatch.
>I think the problem is located in the  output= "nearestStart" because
>"overlapping" produces the correct result. Specifically the second line
>of the annPeak output should be assigning peak1 to overlapEnd instead of
>overlapStart because the gene feature is located on the negative strand.
>
>
>
>Matt
>
>
>> library(ChIPpeakAnno)
>>
>>
>> 
>>peak<-RangedData(IRanges(start=as.numeric(as.character(c(1650,2806,8361))
>>), end=as.numeric(as.character(c(1860,3006,8591)))),
>>space=c("Chr01","Chr01","Chr01"),strand=as.integer(1))
>> row.names(peak)<-c("peak1","peak2","peak3")
>>
>>
>> #load subset of data from Populus v210 gff3 file
>> genome<-as.data.frame(rbind(c("Chr01","phytozome8_0",
>>"gene",1660,2502, ".",     "-",     ".","Potri.001G000100"),c("Chr01",
>>"phytozome8_0",     "gene",2906,6646,    ".",        "-",
>>".","Potri.001G000200"),c("Chr01", "phytozome8_0",   "gene",8391,8860,
>>".",     "+",     ".","Potri.001G000300")))
>>
>>
>
>> GENOME<-GFF2RangedData(genome)
>
>Warning message:
>
>In DataFrame(...) : NAs introduced by coercion
>
>> row.names(GENOME)<-genome[,9]
>>
>>   annPeak = annotatePeakInBatch(peak, AnnotationData=GENOME,
>>PeakLocForDistance ="middle",output="both")
>Warning messages:
>1: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion
>2: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion
>>
>> View(annPeak)
>
>space
>
>start
>
>end
>
>width
>
>names
>
>peak
>
>strand
>
>feature
>
>start_position
>
>end_position
>
>insideFeature
>
>distancetoFeature
>
>shortestDistance
>
>Chr01
>
>8361
>
>8591
>
>231
>
>peak3 Potri.001G000300
>
>peak3
>
>+
>
>Potri.001G000300
>
>8391
>
>8860
>
>overlapStart
>
>85
>
>30
>
>Chr01
>
>1650
>
>1860
>
>211
>
>peak1 Potri.001G000100
>
>peak1
>
>-
>
>Potri.001G000100
>
>1660
>
>2502
>
>overlapStart
>
>747
>
>10
>
>Chr01
>
>2806
>
>3006
>
>201
>
>peak2 Potri.001G000100
>
>peak2
>
>-
>
>Potri.001G000100
>
>1660
>
>2502
>
>downstream
>
>-404
>
>304
>
>Chr01
>
>2806
>
>3006
>
>201
>
>peak2 Potri.001G000200
>
>peak2
>
>-
>
>Potri.001G000200
>
>2906
>
>6646
>
>overlapEnd
>
>3740
>
>100
>
>
>
>>
>> sessionInfo()
>R version 3.1.0 (2014-04-10)
>Platform: x86_64-pc-linux-gnu (64-bit)
>
>locale:
>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=C            LC_COLLATE=C
> [5] LC_MONETARY=C        LC_MESSAGES=C
> [7] LC_PAPER=C           LC_NAME=C
> [9] LC_ADDRESS=C         LC_TELEPHONE=C
>[11] LC_MEASUREMENT=C     LC_IDENTIFICATION=C
>
>attached base packages:
>[1] grid      parallel  stats     graphics  grDevices utils
>[7] datasets  methods   base
>
>other attached packages:
>[1] ChIPpeakAnno_2.13.1  Biostrings_2.32.1
> [3] XVector_0.4.0        IRanges_1.22.10
> [5] biomaRt_2.20.0       VennDiagram_1.6.7
> [7] GOSemSim_1.22.0      Rcpp_0.11.2
> [9] BiocInstaller_1.14.2 edgeR_3.6.7
>[11] limma_3.20.8         hash_2.2.6
>[13] GSEABase_1.26.0      annotate_1.42.1
>[15] GOstats_2.30.0       graph_1.42.0
>[17] Category_2.30.0      GO.db_2.14.0
>[19] RSQLite_0.11.4       DBI_0.2-7
>[21] Matrix_1.1-4         AnnotationDbi_1.26.0
>[23] GenomeInfoDb_1.0.2   Biobase_2.24.0
>[25] BiocGenerics_0.10.0
>
>loaded via a namespace (and not attached):
>[1] AnnotationForge_1.6.1   BBmisc_1.7
> [3] BSgenome_1.32.0         BatchJobs_1.3
> [5] BiocParallel_0.6.1      GenomicAlignments_1.0.5
>[7] GenomicFeatures_1.16.2  GenomicRanges_1.16.4
> [9] MASS_7.3-33             RBGL_1.40.0
>[11] RCurl_1.95-4.3          Rsamtools_1.16.1
>[13] XML_3.98-1.1            bitops_1.0-6
>[15] brew_1.0-6              checkmate_1.2
>[17] codetools_0.2-8         digest_0.6.4
>[19] fail_1.2                foreach_1.4.2
>[21] genefilter_1.46.1       iterators_1.0.7
>[23] lattice_0.20-29         multtest_2.20.0
>[25] rtracklayer_1.24.2      sendmailR_1.1-2
>[27] splines_3.1.0           stats4_3.1.0
>[29] stringr_0.6.2           survival_2.37-7
>[31] tools_3.1.0             xtable_1.7-3
>[33] zlibbioc_1.10.0
>
>
>>
>
>
>
>
>
>
>From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu]
>Sent: Wednesday, August 13, 2014 2:47 PM
>To: Zinkgraf, Matthew S -FS
>Cc: bioconductor at r-project.org
>Subject: Re: ChIPpeakAnno 2.12.2 bug
>
>Matt,
>
>Many thanks for helping us identifying the bug introduced in 2.12.2! The
>bug has been fixed in version 2.13.1. Please let me know if you have any
>issues.
>
>For future correspondence, could you please keep the discussion in the
>bioconductor list so others can contribute or benefit? Thanks!
>
>Best regards,
>
>Julie
>
>On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at fs.fed.us>
>wrote:
>Hello Julie
>I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am
>getting incorrect results from annotatePeakInBatch.
>More specifically the output column 'insideFeature' is not taking feature
>strand into account when it is assigning peaks to gene features, the
>function thinks all gene features are on the positive strand even though
>my genome ranged data contains strand information. Also all other
>calculations from annotatePeakInBatch gives the same results as in 2.10.
>
>Please let me know if you would like more information about the bug I am
>getting.
>Thanks
>
>Matt
>
>
>---
>
>Matthew S. Zinkgraf, PhD
>Postdoctoral Researcher
>USDA, Forest Service
>Davis, CA 95618
>530-759-1739
>mszinkgraf at fs.fed.us <mailto:mszinkgraf at fs.fed.us>
>
>
>
>
>
>
>
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