[BioC] ChIPpeakAnno to find peaks nearest to miRNA

[Zhu, Lihua (Julie)]

Paolo,

Could you please send us a few rows of miRNAs in annotatedPeaks? Thanks!

Best regards,

Julie 
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Paolo Kunderfranco [paolo.kunderfranco at gmail.com]
Sent: Friday, July 27, 2012 5:50 AM
To: bioconductor at r-project.org
Subject: [BioC] ChIPpeakAnno to find peaks nearest to miRNA

Dear All,
I would like to use ChIPpeakAnno to find peaks nearest to miRNA.

I loaded my bed file and created a ranged data, load
mmusculus_gene_ensembl dataset through mart and annotated my peaks,
and it seems ok,

test.rangedData = BED2RangedData(test.bed)
mart<-useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl")
Annotation = getAnnotation(mart, featureType="miRNA")
annotatedPeak = annotatePeakInBatch(test.rangedData, AnnotationData=Annotation)
as.data.frame(annotatedPeak)

<factor>            <IRanges> |   <character> <character>
<character>      <numeric>    <numeric>   <character>
MACS_peak_109 ENSMUSG00000089245        1 [54494876, 54496209] |
MACS_peak_109           + ENSMUSG00000089245       54826062
54826166      upstream
numeric>        <numeric>              <character>
-331186           329853             NearestStart


Now I would like to add miRNA Id as I already did when I annotated for
TSS, but something goes wrong, any ideas how to solve it?

library("org.Mm.eg.db")
b<- addGeneIDs(annotatedPeak,"org.Mm.eg.db",c("symbol"))
Error: No entrez identifier can be mapped by input data based on the
feature_id_type. Please consider to use correct feature_id_type,
orgAnn or annotatedPeak


Thanks,

Paolo


> traceback()
2: stop("No entrez identifier can be mapped by input data based on the
feature_id_type.\nPlease consider to use correct feature_id_type,
orgAnn or annotatedPeak\n",
       call. = FALSE)
1: addGeneIDs(annotatedPeak, "org.Mm.eg.db", c("symbol"))
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] targetscan.Mm.eg.db_0.5.0           BiocInstaller_1.4.7
      org.Mm.eg.db_2.7.1                  ChIPpeakAnno_2.4.0
 [5] limma_3.12.1                        org.Hs.eg.db_2.7.1
      GO.db_2.7.1                         RSQLite_0.11.1
 [9] DBI_0.2-5                           AnnotationDbi_1.18.1
      BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0
[13] GenomicRanges_1.8.7                 Biostrings_2.24.1
      IRanges_1.14.4                      multtest_2.12.0
[17] Biobase_2.16.0                      biomaRt_2.12.0
      BiocGenerics_0.2.0                  gplots_2.11.0
[21] MASS_7.3-19                         KernSmooth_2.23-8
      caTools_1.13                        bitops_1.0-4.1
[25] gdata_2.11.0                        gtools_2.7.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1.1   splines_2.15.0   stats4_2.15.0
survival_2.36-14 tools_2.15.0     XML_3.9-4.1

_______________________________________________
Bioconductor mailing list
Bioconductor at r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor