Re: ChIPpeakAnno 2.12.2 bug

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" <[email protected]> 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-3WprALB+yeL2fBVCVOL8/[email protected]]
>Sent: Wednesday, August 13, 2014 2:47 PM
>To: Zinkgraf, Matthew S -FS
>Cc: [email protected]
>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" <[email protected]>
>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
>[email protected] <mailto:[email protected]>
>
>
>
>
>
>
>
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