Hello, 

I am trying to identify all putative GATA binding sites in the mouse genome.  Ideally, I want to get genomic coordinates for each "binding site" to enter into a GenomicRanges object (I know there will be a lot of hits) and to overlay this information with the results of a ChIP-Seq experiment. Seems that there are multiple packages to try and do this with, but only RMAPPER allows an interface with the TRANSFAC and Jaspar TF binding site models. 
I have been getting multiple errors that I am not sure how to resolve.  Is this package the best way to get the information I want?  Is there a better alternative?  Is there an upper limit to the MAPPER query?

Thanks for your help, 
Ravi

#load the necessary libraries
library (RMAPPER)
library (biomaRt)

#Compute the mouse genome
#get identifiers to be input into MAPPER
mm = useMart (biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
mmGenes = getBM (attributes = c ("ensembl_gene_id", "external_gene_id", "entrezgene", "external_transcript_id"), mart = mm)
#get list of all entrez gene id's
egids = unique (mmGenes$entrezgene); egids = egids [2:length (egids)] #first id is NA

#make a list of all geneids
eglist = paste (egids [500:550], collapse = ",")

#get the factor models
gata = "M00789, T02689, T00311, T00306, T00305, T00267, T00305, T00267, T00306, T00311, M00632, M00462, MA0037"

#Run MAPPER with 50 genes
gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000)

>Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : cannot open: HTTP status was '0 (null)'

#Run MAPPER with 10 genes
eglist = paste (egids [500:510], collapse = ",")
gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000)

> Error in seq.default(1, nh * 4, 4) : wrong sign in 'by' argument


> traceback ()
10: stop("wrong sign in 'by' argument")
9: seq.default(1, nh * 4, 4)
8: seq(1, nh * 4, 4)
7: `[.data.frame`(df, seq(1, nh * 4, 4), )
6: df[seq(1, nh * 4, 4), ]
5: reshapeMapper(tmp)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("mapperHits", query = sett, hits = reshapeMapper(tmp))
1: readMAPPER(gene = eglist, models = gata, org = "Mm", pbases = 5000)

> sessionInfo ()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.8.0 RMAPPER_1.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.5-0  tools_2.13.0 XML_3.2-0   




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