[BioC] Problem with RIPSeeker

[Nicola Cole]

Hi,

It finally worked for me.  

Nicola



On Aug 15, 2013, at 11:00 AM, Nicola Cole <ncole at utexas.edu> wrote:

> Hi,
> 
> I am trying to use RIPSeeker with bam files generated from Arabidopsis.  I have emailed the author numerous times, and she has finally referred me to you all.
> 
> The error I am getting is:
> 
> Error in useMart(dataset = biomaRt_dataset, ...) : 
>  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart
> Execution halted
> 
> The script I am using is:
> 
> #!/bin/bash
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("RIPSeeker")
> library(RIPSeeker)
> biocLite("biomaRt")
> library(biomaRt)
> biocLite("ChIPpeakAnno")
> biocLite("GenomicFeatures")
> library(GenomicFeatures)
> library(GenomicRanges)
> library(rtracklayer)
> 
> bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for_RIPSeek/Temp_Bam_Files/","\\.bam$",
> recursive=TRUE, full.names=TRUE)
> cName <- "Control_ "
> outDir<-file.path(getwd(),"Nicola_4G_out")
> binSize<-NULL
> minBinSize <- 10000
> maxBinSize <- 10100
> multicore <- TRUE
> strandType <-NULL
> biomart <- "ENSEMBL_MART_PLANT"
> biomaRt_dataset <- "athaliana_eg_gene"
> goAnno <- "org.At.tair.db"
> 
> seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName,
> reverseComplement = TRUE,strandType = strandType,
> uniqueHit = TRUE, assignMultihits = TRUE,
> rerunWithDisambiguatedMultihits = TRUE,
> binSize=binSize, minBinSize = minBinSize,
> maxBinSize = maxBinSize,
> biomart=biomart,
> biomaRt_dataset = biomaRt_dataset, goAnno = goAnno,
> multicore=multicore, outDir=outDir)
> 
> q()
> 
> While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error:
> 
> Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org",  : 
>  object 'ENSEMBL_MART_PLANT' not found
> 
> 
> Can you tell me what needs changing in my script?
> 
> Thank  you,
> 
> Nicola Cole
> Browning Lab
> PhD candidate
> UT Ausitn
>