Question: CNV analysis with cghMCR/CNTools
0
gravatar for Tim Smith
9.2 years ago by
Tim Smith1.1k
Tim Smith1.1k wrote:
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 > [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.2 years ago by John Zhang2.9k • written 9.2 years ago by Tim Smith1.1k
Answer: CNV analysis with cghMCR/CNTools
0
gravatar for John Zhang
9.2 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
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 >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-IronPort-Anti-Spam-Filtered: true >X-IronPort-Anti-Spam-Result: As8AAFmDXUuBhJEPkWdsb2JhbACBWJAMiiUBAQEBCQsKBxMFsCWBQIQ0iEQBBAQBhDQE >X-IronPort-AV: E=Sophos;i="4.49,340,1262581200"; d="scan'208";a="299363950" >X-SBRS: 4.5 >X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=-6.6 required=5.0 tests=BAYES_00, DKIM_SIGNED, DKIM_VERIFIED, HTML_MESSAGE, RCVD_IN_DNSWL_MED autolearn=ham version=3.2.5 >DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1264448596; bh=EOtgo27xLH4/qqr0xUl+wZq4G5nnaurJkhbhzFHm3Sk=; h=Message-ID:X-YMail-OSG:Received:X-Mailer:Date:From:Subject:To:MIME- Version:Con tent-Type; b=gr60cy/N4B1ut8rAWwZn2ILzscEIgucVJ+0txYmijVsBF+bsF/beDwQENtvg3N4RihUo iZVW53nvk+ 6AMiwPAOW3G5OamUjbdHzZQYPpOAJ50VqOT49a8Krn4UoV96jYEpW3928cbnX8Vy8Kf/VL XCP5ZlOjIu YsW+i4H2htLhg= >DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:X-YMail-OSG:Received:X-Mailer:Date:From:Subject:To:MIME- Version:Con tent-Type; b=qXJXKIXfAhVj4rW4rR30q9iGiMqum1g3BLlL4XuP9RMI0n5kHJ1n6SYxrq7ubpQ/SA0b P31Xja2Kr+ JV9ULt3UoIPHqk8un5mXzKWep9mVAZjZFBsuziNC0o3mhO2G7d3lYxPCWRVZLuKV6CMk0D VzZp1xwWkK u0qJ6SG9VJ5GM=; >X-YMail-OSG: LUvHYgQVM1moD.z.t3NmZrTrlfhLU1REGPkwV6bAuvEnZkWUossPX2BP3vlRrJA1YknPjG 2UffWYt6DU TrZo4nj4IdfweaU2I40ijShbgOfY1stQNJ8LuM3TM1iPX93nVBj2HLAyGlNYsGrwgxAmWH KxWsRZlIRX y83i6hAEAkYCI_fVR6iSsyGVXL5zuBpbBSn8jdz_QAieb.7lPcJXpkld.rLP3Dshha7qVl 9uMj2IVUsV qO3IrXy87YoBMqsg_HJ8RG9iPL.5hucwgjqIh6UO8l5tNvYAIoqYmrHUBDoyboprXNge4f PD8XrJBny9 rVgcxIaF87c1rhA6siVATHMwuv1hoIpW7.y3kjRtp2xogR.etUxnQNrSLfI.SseSAZGUQg w3EiqDbHhM I_jkubw7PboZWAq9DfDICz0ONNoSWaFIBTweXrbEFQX4Z550_cI- >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=""> >MIME-Version: 1.0 >X-Tag-Only: YES >X-Filter-Node: phil3.ethz.ch >X-USF-Spam-Level: - >X-USF-Spam-Status: hits=-1.5 tests=BAYES_00, DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST, FROM_HAS_ULINE_NUMS, HTML_30_40, HTML_MESSAGE >X-USF-Spam-Flag: NO >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Content-Disposition: inline >Subject: [BioC] CNV analysis with cghMCR/CNTools >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.13 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" options="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit > >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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 9.2 years ago by John Zhang2.9k
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