[BioC] Problem with RIPSeeker
Nicola Cole
ncole at utexas.edu
Thu Aug 15 18:00:00 CEST 2013
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
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