[BioC] CNV analysis with cghMCR/CNTools

John Zhang jzhang at jimmy.harvard.edu
Mon Jan 25 21:14:29 CET 2010 

Hi, Tim,

Sorry, there is something missing in the Vignette. The following should whork:

GOIGains <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
                      "gains"]))) > 20), "gains"]
GOILosses <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
                      "losses"]))) < -20), "losses"]

I will update the vignette.


JZ

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>Date: Mon, 25 Jan 2010 11:43:16 -0800 (PST)
>From: Tim Smith <tim_smith_666 at yahoo.com>
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>Subject: [BioC] CNV analysis with cghMCR/CNTools
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>Hi,
>
>I wanted to use the cgh package to run CNV analysis. Essentially I want the 
regions/genes showing gains and losses. I am using the code provided in the 
'cghMCR' package vignette, but I'm not sure if the end result is what it should 
be. The code is:
>#################
>##
>## Vignette: cghMCR
>## Pdf at: 
http://www.bioconductor.org/packages/bioc/vignettes/cghMCR/inst/doc/findMCR.pdf
>##
>#################
>
>### Section 4: Identifying Segment Gain Or Loss (SGOL)
>
>library(cghMCR)
>library(limma)
>library(DNAcopy)
>library(CNTools)
>
>require(CNTools, quietly = TRUE)
>data("sampleData", package = "CNTools")
>head(sampleData)
>
>data(geneInfo)
>data(sampleData, package = "CNTools")
>set.seed(1234)
>convertedData <- getRS(CNSeg(sampleData[which(is.element(sampleData[,
>                  "ID"], sample(unique(sampleData[, "ID"]), 20))), ]), by = 
"gene",
>                  imput = FALSE, XY = FALSE, geneMap = geneInfo)
>
>require(cghMCR, quietly = TRUE)
>SGOLScores <- SGOL(convertedData, threshold = c(-0.2, 0.2), method = sum)
>plot(SGOLScores)
>
>#Based on the SGOL scores, genes in regions of gains or losses can be obtained 
by a
>#set of thresholds, say -20 and 20.
>
>GOIGains <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
>                      ]))) > 20), "gains"]
>GOILosses <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
>                      ]))) < -20), "losses"]
>head(gol(GOIGains))
>>         gains
>169270 0.8809
>644147 0.8809
>26260  0.8809
>157695 0.3416
>389607 0.3416
>157697 0.3416
>
>------------------------------------------
>Shouldn't this return genes that have "gains" > 20 ? Similarly, 
'head(gol(GOILosses))' doesn't appear to be giving genes that have a SGOL score 
< -20.
>thanks!
>My sessionInfo():
>> sessionInfo()
>R version 2.10.0 (2009-10-26) 
>i386-pc-mingw32 
>
>locale:
>[1] LC_COLLATE=English_United States.1252 
>[2] LC_CTYPE=English_United States.1252   
>[3] LC_MONETARY=English_United States.1252
>[4] LC_NUMERIC=C                          
>[5] LC_TIME=English_United States.1252    
>
>attached base packages:
>[1] stats     graphics  grDevices utils     datasets  methods   base     
>
>other attached packages:
> [1] cghMCR_1.4.0         limma_3.2.1          CNTools_1.2.0       
> [4] DNAcopy_1.20.0       int.geneint.db_1.1.1 PAnnBuilder_1.8.0   
> [7] GOstats_2.12.0       graph_1.24.1         Category_2.12.0    
>[10] GO.db_2.3.5          multtest_2.2.0       minet_2.0.0         
>[13] infotheo_1.1.0       fExtremes_2100.77    fTrading_2100.76    
>[16] fGarch_2110.80       fBasics_2100.78      MASS_7.3-3          
>[19] timeSeries_2110.87   timeDate_2110.87     R.utils_1.2.4       
>[22] R.oo_1.6.5           R.methodsS3_1.0.3    XML_2.6-0           
>[25] genefilter_1.28.0    hgu95av2.db_2.3.5    hgu133a.db_2.3.5    
>[28] org.Hs.eg.db_2.3.6   RSQLite_0.7-3        DBI_0.2-4           
>[31] AnnotationDbi_1.8.0  GEOquery_2.8.0       RCurl_1.2-1         
>[34] bitops_1.0-4.1       biomaRt_2.2.0        affy_1.24.1         
>[37] Biobase_2.6.0       
>
>loaded via a namespace (and not attached):
>[1] affyio_1.14.0        annotate_1.24.0      GSEABase_1.8.0     
>[4] preprocessCore_1.8.0 RBGL_1.20.0          splines_2.10.0     
>[7] survival_2.35-7      tools_2.10.0         xtable_1.5-6        
>> 
>
>
>      
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>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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