[BioC] ChIPpeakAnno problem w getAllPeakSequence()

[Anna Ehrlund]

Hi Jianhong,

Thanks so much for your help, your suggestion to use the BSgenome as annotaionData worked perfectly. Problem solved for me.

The bioMart-dependent code still fails on the same data set, not sure why, perhaps a glitch in my bioMart connection or something (no other network problems here though). I'll send you a subset of my data (that fails) off-list if you want to try and reproduce the problem.

Again, thanks for your quick help!

Anna
________________________________________
Från: Ou, Jianhong [Jianhong.Ou at umassmed.edu]
Skickat: den 17 oktober 2012 18:22
Till: Anna Ehrlund
Cc: <bioconductor at r-project.org>
Ämne: Re: [BioC] ChIPpeakAnno problem w getAllPeakSequence()

Hi Anna,

And a better way to resolve your problem is that use BSgenome as annotationData for getAllPeakSequence() function. Try,

library(BSgenome.Hsapiens.UCSC.hg19)
peaksequences <- getAllPeakSequence(mergedpeakannotations,  upstream=100, downstream=100, genome=Hsapiens)

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Oct 17, 2012, at 12:03 PM,  wrote:

> Hi Anna,
>
> To get the peak sequences you can try BSgenome + BStrings first. Try ?getSeq to extract the sequence from local database, faster than remote mart.
>
> Because I can not repeat your error, could you please share the subset of you data to me for testing?
>
> Yours sincerely,
>
> Jianhong Ou
>
> jianhong.ou at umassmed.edu
>
>
> On Oct 17, 2012, at 9:14 AM, Anna Ehrlund wrote:
>
>> Dear list,
>>
>> I've just started analyzing a ChIP-seq data set. I generated a peak list using "standard" utilities (bowtie, MACS) and loaded it into R in the ChIPpeakAnno package. I managed to annotate the peaks but when I tried to retrieve the peak sequences using the getAllPeakSequence() function I ran into a problem:
>>
>>
>> peaksequences<-getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=mart, AnnotationData=getAnnotation(mart, featureType="TSS"))
>> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
>> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
>>
>> The error message sometimes states downstream_flank instead of upstream. At one point I got it to run on a small subset of the data (first 10 rows) but later the same command failed with this same error message.
>>
>> Some info about the objects:
>> mergedpeakannotations: RangedData object, created using mergedpeakannotations<- annotatePeakInBatch(mergedpeak.rd, AnnotationData=getAnnotation(mart, featureType="TSS"))
>>
>> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
>>
>> Anybody got a clue about why this fails? All help would be much appreciated!
>>
>> Best regards!
>> Anna
>>
>>
>>
>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
>> [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
>> [5] LC_TIME=Swedish_Sweden.1252
>>
>> attached base packages:
>> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] ChIPpeakAnno_2.6.0                  limma_3.14.1
>> [3] org.Hs.eg.db_2.8.0                  GO.db_2.8.0
>> [5] RSQLite_0.11.2                      DBI_0.2-5
>> [7] AnnotationDbi_1.20.1                BSgenome.Ecoli.NCBI.20080805_1.3.17
>> [9] BSgenome_1.26.1                     GenomicRanges_1.10.2
>> [11] Biostrings_2.26.2                   IRanges_1.16.2
>> [13] multtest_2.14.0                     Biobase_2.18.0
>> [15] biomaRt_2.14.0                      BiocGenerics_0.4.0
>> [17] VennDiagram_1.5.1
>>
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-22      parallel_2.15.1  RCurl_1.95-1.1   splines_2.15.1   stats4_2.15.1
>> [6] survival_2.36-14 tools_2.15.1     XML_3.95-0.1
>>
>>
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>>
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