[Bioc-sig-seq] Rsamtools append

[burak kutlu]

Hi 
Following the example given in this thread:
http://www.mail-archive.com/bioc-sig-sequencing@r-project.org/msg00805.html
I am trying to "append" the scanned bam files, but somehow I can't.
The code runs but I only have reads from the first chromosome
Any ideas?
Many thanks in advance
-burak

Here's what I am trying to do:

my.bam.file <- paste(barcodeDir, "/", bfFiles[2], "/output/mapping/solid0444_20100121_bcSample1_F3.bam",sep="")
lens <- org.Mm.egCHRLENGTHS
lens <- lens[c(1:19,"X","Y")]
i=2
which <- RangesList(IRanges(start=1,end=lens[i]))
names(which) <- paste("chr",names(lens)[i],sep="")
params <- ScanBamParam(which=which)
myReads <<- scanBam(my.bam.file,param=params)
for(i in c(2:length(lens))){
      which <- RangesList(IRanges(start=1,end=lens[i]))
      names(which) <- paste("chr",names(lens)[i],sep="")
      params <- ScanBamParam(which=which)
      myReads <<- append(myReads,scanBam(my.bam.file,param=params)[[1]])
}#i




R version 2.11.0 alpha (2010-03-29 r51485) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] rtracklayer_1.7.11                      
 [2] RCurl_1.3-1                             
 [3] bitops_1.0-4.1                          
 [4] Rsamtools_0.2.0                         
 [5] ggplot2_0.8.7                           
 [6] digest_0.4.2                            
 [7] reshape_0.8.3                           
 [8] plyr_0.1.9                              
 [9] proto_0.3-8                             
[10] org.Mm.eg.db_2.4.0                      
[11] RSQLite_0.8-4                           
[12] DBI_0.2-5                               
[13] AnnotationDbi_1.9.6                     
[14] Biobase_2.7.5                           
[15] ShortRead_1.5.21                        
[16] lattice_0.18-3                          
[17] BSgenome.Mmusculus.UCSC.mm9_1.3.16      
[18] BSgenome_1.15.20                        
[19] GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2
[20] GenomicFeatures_0.5.1                   
[21] GenomicRanges_0.1.0                     
[22] Biostrings_2.15.26                      
[23] IRanges_1.5.73                          

loaded via a namespace (and not attached):
[1] biomaRt_2.3.5 hwriter_1.2   tools_2.11.0  XML_2.8-1