[BioC] readPositionalInfo in snapCGH for preparing CNA files for DNAcopy

[Bernard North [guest]]

Dear All,
 
I am working on Agilent 244k aCGH files and am ultimately segmenting them with DNAcopy.
I have succeeded in doing this by creating the CNA files that DNAcopy’s smooth.CNA function needs but I wonder if this is the right strategy as I required the readPositionalInfo function from another package, snapCGH, to create those files and encountered some problems.
I needed readPositionalInfo to create Chr and Position fields for the CNA object but the function errored and needed fixing.
The first problem was that readPositionalInfo contains this line at the end of a switch section :
“stop("Source argument not recognised"), )” 
The comma (penultimate character) seems to tell R that there are two defaults and results in the error "duplicate switch defaults: 'stop("Sour...' and ''"
This seems to have been reported elsewhere:
http://grokbase.com/t/r/bioconductor/128r956jfk/bioc-readpositionalinfo
 
Another issue seems to be that readPositionalInfo doesn't actually create a variable called Position (of gene - it creates variables called start and end instead) which creates problems when subsequently using the MAList object in processCGH or to create a CNA object for segmenting in DNAcopy. This has been found before  https://stat.ethz.ch/pipermail/bioconductor/2009-September/029519.html
I fixed this as other have done by creating position to be (start+end)/2.
 
I wondered if the steps I have used are correct and standard as I am surprised that a commonly used function would apparently have errors or require work-arounds. Or maybe I am using it incorrectly.
Many thanks in advance for any specific or general advice on my analysis
 
Bernard North


 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: i386-w64-mingw32/i386 (32-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] stats     graphics  grDevices utils     datasets  methods   base     
 
other attached packages:
[1] snapCGH_1.30.0       DNAcopy_1.34.0       limma_3.16.5        
[4] BiocInstaller_1.10.2
 
loaded via a namespace (and not attached):
[1] aCGH_1.38.0           affy_1.38.1           affyio_1.28.0        
 [4] annotate_1.38.0       AnnotationDbi_1.22.6  Biobase_2.20.1       
 [7] BiocGenerics_0.6.0    cluster_1.14.4        DBI_0.2-7            
[10] genefilter_1.42.0     GLAD_2.24.0           grid_3.0.0           
[13] IRanges_1.18.1        lattice_0.20-15       MASS_7.3-27          
[16] multtest_2.16.0       parallel_3.0.0        pixmap_0.4-11        
[19] preprocessCore_1.22.0 RColorBrewer_1.0-5    RSQLite_0.11.4       
[22] splines_3.0.0         stats4_3.0.0          strucchange_1.4-7    
[25] survival_2.37-4       tilingArray_1.38.0    tools_3.0.0          
[28] vsn_3.28.0            XML_3.98-1.1          xtable_1.7-1         
[31] zlibbioc_1.6.0       


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