[BioC] Problem with RIPSeeker

[Nicola Cole]

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