[BioC] readGappedAlignments not working in Rsamtools

[Alvaro [guest]]

Hello everybody,

I'm a PhD student and I am doing my first analysis on RNAseq data.

I was trying to use the script to generate a table of counts from bam files (shown here):

library(Rsamtools)

setwd("C:/R_data")

bam_files <- list.files(pattern="*.bam")
gr_list <- lapply(bam_files,
                  function(bam_file)
                    as(readGappedAlignments(bam_file), "GRanges"))
names(gr_list) <- bam_files

library(GenomicFeatures) 
txdb=makeTranscriptDbFromUCSC(genome='dm3',tablename='ensGene')

tx_by_gene=transcriptsBy(txdb,'gene')
ex_by_gene=exonsBy(txdb,'gene')
toc=data.frame(rep(NA,length(tx_by_gene)))
for(i in 1:length(bam_files))
{
  toc[,i]=countOverlaps(tx_by_gene,bam_files[[i]])
}
rownames(toc)=names(tx_by_gene)
colnames(toc)=names(gr_list)
dim(toc)
head(toc)

But it doesn't seem to work, failing in two places:

1) Error in .class1(object) : could not find function "readGappedAlignments"

2) Download the ensGene table ... Error in function (type, msg, asError = TRUE)  : couldn't connect to host

For the point 1) I found that the function is deprecated but I still can't make things work changing it for the new function that is supposed to replace it "readGAlignmentsFromBam", Can anybody help me fixing this?

The error in part 2) is completely out of my reach at the moment, I don't know how to fix this issue either, so any help would be appreciated.

Thanks in advance!

     

 -- output of sessionInfo(): 


R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] GenomicFeatures_1.16.2 AnnotationDbi_1.26.0   Biobase_2.24.0        
 [4] Rsamtools_1.16.0       Biostrings_2.32.0      XVector_0.4.0         
 [7] GenomicRanges_1.16.3   GenomeInfoDb_1.0.2     IRanges_1.22.8        
[10] BiocGenerics_0.10.0   

loaded via a namespace (and not attached):
 [1] BatchJobs_1.2           BBmisc_1.6              BiocParallel_0.6.1     
 [4] biomaRt_2.20.0          bitops_1.0-6            brew_1.0-6             
 [7] BSgenome_1.32.0         codetools_0.2-8         DBI_0.2-7              
[10] digest_0.6.4            fail_1.2                foreach_1.4.2          
[13] GenomicAlignments_1.0.1 iterators_1.0.7         plyr_1.8.1             
[16] Rcpp_0.11.1             RCurl_1.95-4.1          RSQLite_0.11.4         
[19] rtracklayer_1.24.2      sendmailR_1.1-2         stats4_3.1.0           
[22] stringr_0.6.2           tools_3.1.0             XML_3.98-1.1           
[25] zlibbioc_1.10.0 

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