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="">
>To: bioc <bioconductor at="" stat.math.ethz.ch="">
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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/fi
ndMCR.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
>>
>
>
>
> [[alternative HTML version deleted]]
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
