I'm sure you did get a result. What happens if you type count16 and press Enter ? Also, you can write your code better.


dataList <- lapply(seqnames(Hsapiens)[16:18], function(chrName) loadAllData(files, chrName)) # Read in data for 3 chromosomes

dataList[[1]] # Look at data for the first chromosome that was used.

dataList[[3]] # Look at data for the last chromosome that was used.


--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
________________________________
From: Asma rabe <asma.rabe@gmail.com>
Sent: Tuesday, 15 July 2014 9:03 PM
To: Dario Strbenac
Cc: Bioconductor@r-project.org
Subject: Re: [BioC] deepSNV Question

Hello Dario,

Thank you for help.

I have tried looping on chromosomes one by one (tried 3 chromosomes for testing) but I got no result as follows....


seq<-as(seqinfo(Hsapiens), "GRanges")


seq


GRanges with 93 ranges and 0 metadata columns:

                       seqnames         ranges strand

                          <Rle>      <IRanges>  <Rle>

            chr1           chr1 [1, 249250621]      *

            chr2           chr2 [1, 243199373]      *

            chr3           chr3 [1, 198022430]      *

            chr4           chr4 [1, 191154276]      *

            chr5           chr5 [1, 180915260]      *

             ...            ...            ...    ...

  chrUn_gl000245 chrUn_gl000245     [1, 36651]      *

  chrUn_gl000246 chrUn_gl000246     [1, 38154]      *

  chrUn_gl000247 chrUn_gl000247     [1, 36422]      *

  chrUn_gl000248 chrUn_gl000248     [1, 39786]      *

  chrUn_gl000249 chrUn_gl000249     [1, 38502]      *

  ---

  seqlengths:

                    chr1                  chr2 ...        chrUn_gl000249

               249250621             243199373 ...                 38502


for (i in 16:18){assign(paste("count",i,sep=""),loadAllData(files,seq[i]))}

count16

 [ reached getOption("max.print") -- omitted 10 matrix slice(s) ]



Any help is appreciated



On Tue, Jul 15, 2014 at 11:00 AM, Dario Strbenac <dstr7320@uni.sydney.edu.au<mailto:dstr7320@uni.sydney.edu.au>> wrote:
Hello,

You will need more than 4 GB RAM to do the analysis. Can you find another computer with more memory ? Also, make sure you are not using 32-bit R. You need 64-bit R and an operating system which is 64-bit to be able to access more RAM.

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia


	[[alternative HTML version deleted]]

