Entering edit mode
Paolo Kunderfranco
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350
@paolo-kunderfranco-5158
Last seen 7.2 years ago
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