version 1.1.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PharmacoGx
 Type: Package
-Title: Large-Scale Analysis of Pharmacogenomic Data
-Version: 1.0.6
-Date: 2015-07-23
+Title: Analysis of Large-Scale Pharmacogenomic Data
+Version: 1.1.2
+Date: 2015-11-13
 Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
 Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
 Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
@@ -12,9 +12,7 @@ Encoding: UTF-8
 Imports: Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
         methods, downloader, stats, utils, graphics, grDevices
 Depends: R (>= 2.10)
-URL: http://www.pmgenomics.ca/bhklab/software/pharmacogx
-LazyData: yes
 NeedsCompilation: no
-Packaged: 2015-07-23 21:59:54 UTC; haibeb
+Packaged: 2015-11-14 18:15:28 UTC; bhaibeka
 Repository: CRAN
-Date/Publication: 2015-07-24 07:53:45
+Date/Publication: 2015-11-15 10:08:46

MD5

@@ -1,110 +1,106 @@
-9f5555dcbc09672a249f37e736491d26 *DESCRIPTION
-374f15550c7a22af3711c0e99e418bab *NAMESPACE
-fa60061d29d52219592a940b69e31d72 *R/GWC.R
-5dc4cfb09d006998b95ac0c513307ae5 *R/LogLogisticRegression.R
-b9eb1c2d8a3a7e202b2b8f2e71e57224 *R/PharmacoSetClass.R
-27cfdbca54ab12672a8b5d43fd0237e2 *R/callingWaterfall.R
+468d9b492b0f75714e6f7c392b91f701 *DESCRIPTION
+1bd597a4713609793a7c321c1c4f97c6 *NAMESPACE
+4ba01e7c2d015b45f2a13b080103922c *R/GWC.R
+b0a18cff2ece56d6355de297cc3e9b22 *R/LogLogisticRegression.R
+d7b04169a28b6afceaac4e69367a245a *R/PharmacoSetClass.R
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 e496092258e962d83be708d422f5febd *R/combineTest.R
-23a4a6cc5d0230517827cb8cfaa68eb2 *R/computeAUC.R
-e47d124450006f07b20b8de632982f16 *R/computeDrugSensitivity.R
-4d5ab4de072b32fdd94e0ab814a3bb63 *R/computeIC50.R
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-75861da0497751b86447bc3a4a5e8402 *R/datasets.R
-6469dcaf0d018e5bf1298dabb6560c05 *R/distancePointLine.R
-8361cf02cbbf07841b60948e20086e82 *R/distancePointSegment.R
-a14c3174c801721bffc0ac94647d9929 *R/downloadPSet.R
-d4dcb7a4aa49a89f0ed8699cf4da9cdb *R/downloadSignatures.R
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 c3ce0daf64ce4be7f5b598ee43be14ec *R/geneDrugPerturbation.R
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-2aec37d37a7c50d95865d86675dbb388 *R/geneIdMap.R
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-0b56c4b071baef88ce69f32dd8abf6c4 *R/rankGeneDrugPerturbation.R
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-93f580ecca9149de64874d6d8f5b8717 *R/signatureClass.R
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-3c56f2e9feb0c9d4ba688e262da50c0e *R/summarizeGeneExpression.R
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 edcf760dd5ac1afe6aa704ac746b22ec *README
-724c78f4d9f6f02e031c1ca56c6b27ce *build/vignette.rds
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+5bc7d378c90d6616d16d0cccca454353 *data/datalist
 f407e1c5c77e062f1e565f12ef434fff *inst/CITATION
-32fed253d8cd65a4a0f527f4cef40fdb *inst/doc/PharmacoGx.R
-13a8e0afeb4eeabcc7dcccb52c9bbcb6 *inst/doc/PharmacoGx.Rnw
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 ce0ead69148fbe8a31a8af0bf372481b *man/CCLEsmall.Rd
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 63bc5587bf141b425e6eef540d3ab82f *man/CMAPsmall.Rd
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 2db92ae4a4e12104f736e9663cd3cc35 *man/GWC.Rd
 c1bc70c5f4159b6621fe3a3dc73dfdbd *man/HDAC_genes.Rd
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 3da26b01d50e2368ce20d91aea64f5a5 *man/cellInfo-set.Rd
 82f5b39765546bfd630f0b5b49ff96a7 *man/cellInfo.Rd
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 cb3208411e95d1d3c3a96f0466fe51aa *man/dateCreated.Rd
-0ac2a23b9c874ea68077740ee2798b08 *man/dnaData-set.Rd
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-b539f2ee0d76361eab288c47654ed238 *man/downloadPSet.Rd
-8893032d7cfde1b8dc937975b1407a60 *man/downloadSignatures.Rd
-dcbc892e5932c51835d50d50aab71e1b *man/drugDoseResponseCurve.Rd
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 6c31820f8a8ae5f5f3d9099f48de2d02 *man/drugInfo-set.Rd
 4682d85d183bf373e2519775c0506fd4 *man/drugInfo.Rd
 e4542d879d200c0275358f91b90ca77a *man/drugNames-set.Rd
 440214ee9770d1c3517013fa952b545a *man/drugNames.Rd
-0408cd78085e1f7089672a317f37fc29 *man/drugPertubrationSig.Rd
-5614a0a76d09b8c4718fe661ab88a0f8 *man/drugSensitivitySig.Rd
-ba7a844b73e6af267e1cb3c46ab129a4 *man/geneInfo-set.Rd
-2b20e8c2fe9df31ebe7f5c9e7cfc383d *man/geneInfo.Rd
-0c2de30ca146add701f73b1562625e26 *man/geneNames.Rd
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+817e54e4c02ce5e5df3c85286d0a6bfc *man/drugSensitivitySig.Rd
+c7d285717d104f07e893dd5b1da0f166 *man/featureInfo-set.Rd
+4dff8be8cbdfe9f1aab579b55b4b73a2 *man/featureInfo.Rd
+8bfc66f350cbfa1277380f5eeead03b9 *man/featureNames.Rd
 60bc9a3ef18e038ecf69cd32dd56171a *man/intersectList.Rd
-cf3aabe14859b107b62f9c62caea4d62 *man/intersectPSet.Rd
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+176e2487c84c10be0dd4e8e828205bac *man/molecularProfiles-set.Rd
+a451faed39660a81a120a9fc2c4605e8 *man/molecularProfiles.Rd
 fff5f711742cf34676a62827770ee560 *man/pSetName.Rd
 130bdcf2faa71804554dc82c734b341c *man/pertNumber-set.Rd
 c49271974e84b34b308cbdd4034fe730 *man/pertNumber.Rd
-ddfcaa3b224f2f66a1632b210dafffcb *man/probeGeneMapping.Rd
-4129d0601e0ae100b4cc5174336aa467 *man/rnaData-set.Rd
-558811cbeb3a37e4dabaa8e5e835784c *man/rnaData.Rd
-20e1a488059e85bb306e8bf2baec1ccd *man/rnaInfo-set.Rd
-bd24149ea37d7bf194ef7bd6b3a261b1 *man/rnaInfo.Rd
+61d3e2177a3b5ecd071a0557a27495d9 *man/phenoInfo-set.Rd
+171535c0dfd3393cf71f07b21ea51e22 *man/phenoInfo.Rd
 a7ab09b3f118c5ff556bfdee48b9c6eb *man/sensNumber-set.Rd
 49cb7391d881d5d7f5f49eacfff92b7d *man/sensNumber.Rd
-b21716f33a3de57398590cfd3c598d44 *man/sensitivityData-set.Rd
-8fbaa57f6d8fd7c8a8f111ba838a546f *man/sensitivityData.Rd
-677aee26a5f354fb5d4a2e6c8f90138e *man/sensitivityInfo-set.Rd
-1e92d2f7cc4eedc275ec97ea08ff8496 *man/sensitivityInfo.Rd
-ebd0ad39cfc6bf38d01450ea26a4898e *man/sensitivityMeasures.Rd
+0aba37e235ed44221a10535c7716f3d7 *man/sensitivityInfo-set.Rd
+1b54237eb48abda52cadea8bcbabc741 *man/sensitivityInfo.Rd
+ec1808022eec306c5a29545be8c06cb6 *man/sensitivityMeasures.Rd
+a63a058c80a2fc634e03fb23459b48b3 *man/sensitivityProfiles-set.Rd
+82cbc2b282e85febf7d04522ff6bc133 *man/sensitivityProfiles.Rd
 4930a4f1af52f578ef2240e6c4f08df3 *man/show-PharmacoSet-method.Rd
 3ef97409b0ae027eb5b8dcb0ff92d42b *man/show-PharmacoSig-method.Rd
 ffda236e92b4e0dde23a16c66c61479a *man/showSigAnnot.Rd
-d737523b11d7fb64ae5f7b72df967841 *man/snpData-set.Rd
-0886a0c697456f3a5bbf7d9595fc8c13 *man/snpData.Rd
-93c34551538d7ee716727ac032930112 *man/snpInfo-set.Rd
-566347bcf012822fdee7eb8e98c9fdcb *man/snpInfo.Rd
 cd6b81abd508e8d02d542d2319076202 *man/sub-PharmacoSet-method.Rd
-9b0ebf0c3fed989b810c912e5c51d51b *man/subsetTo.Rd
-24523d5601b23afbb5c6920d99d2e900 *man/summarizeGeneExpression.Rd
-725baffeec3fa28e973d6618d23a0425 *man/summarizeSensitivityPhenotype.Rd
+9d55023851d4c3ab1dee6b3cc1c992f4 *man/subsetTo.Rd
+52c2e103079578aa870692529a3ec0a4 *man/summarizeMolecularProfiles.Rd
+3803b0130c2e7bfef5524d4398bd79a4 *man/summarizeSensitivityProfiles.Rd
 457364fbacccbf46552de93a86e7d919 *man/unionList.Rd
-13a8e0afeb4eeabcc7dcccb52c9bbcb6 *vignettes/PharmacoGx.Rnw
+59af8835692df3a4717f32869615bbca *vignettes/CreatingPharmacoSet-concordance.tex
+7e042f996f7c7fa9c8d508f2d4794e74 *vignettes/CreatingPharmacoSet.Rnw
+31bd0238b7785475cfebdcaeaf8cda37 *vignettes/CreatingPharmacoSet.tex
+4b32434639f9eefba19ad8233b37be0f *vignettes/PharmacoGx.Rnw
 0a1c145a5ef73983dbbf130e0ced5379 *vignettes/biblio.bib
+b62b07b83dd4f275fd9eab4e7e9bd0fc *vignettes/pharmacogx.bib

NAMESPACE

@@ -1,72 +1,66 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
 export(PharmacoSet)
+export(availablePSets)
+export(checkPSetStructure)
 export(computeAUC)
+export(computeIC50)
 export(connectivityScore)
 export(downloadPSet)
-export(downloadSignatures)
+export(downloadPertSig)
 export(drugDoseResponseCurve)
-export(drugPertubrationSig)
+export(drugPerturbationSig)
 export(drugSensitivitySig)
 export(gwc)
 export(intersectList)
 export(intersectPSet)
-export(probeGeneMapping)
+export(logLogisticRegression)
 export(showSigAnnot)
 export(subsetTo)
-export(summarizeGeneExpression)
-export(summarizeSensitivityPhenotype)
+export(summarizeMolecularProfiles)
+export(summarizeSensitivityProfiles)
 export(unionList)
 exportMethods("[")
 exportMethods("cellInfo<-")
 exportMethods("cellNames<-")
-exportMethods("cnvData<-")
-exportMethods("cnvInfo<-")
-exportMethods("dnaData<-")
-exportMethods("dnaInfo<-")
 exportMethods("drugInfo<-")
 exportMethods("drugNames<-")
-exportMethods("geneInfo<-")
+exportMethods("featureInfo<-")
+exportMethods("molecularProfiles<-")
 exportMethods("pertNumber<-")
-exportMethods("rnaData<-")
-exportMethods("rnaInfo<-")
+exportMethods("phenoInfo<-")
 exportMethods("sensNumber<-")
-exportMethods("sensitivityData<-")
 exportMethods("sensitivityInfo<-")
-exportMethods("snpData<-")
-exportMethods("snpInfo<-")
+exportMethods("sensitivityProfiles<-")
 exportMethods(cellInfo)
 exportMethods(cellNames)
-exportMethods(cnvData)
-exportMethods(cnvInfo)
 exportMethods(dateCreated)
-exportMethods(dnaData)
-exportMethods(dnaInfo)
 exportMethods(drugInfo)
 exportMethods(drugNames)
-exportMethods(geneInfo)
-exportMethods(geneNames)
+exportMethods(featureInfo)
+exportMethods(featureNames)
+exportMethods(molecularProfiles)
 exportMethods(pSetName)
 exportMethods(pertNumber)
-exportMethods(rnaData)
-exportMethods(rnaInfo)
+exportMethods(phenoInfo)
 exportMethods(sensNumber)
-exportMethods(sensitivityData)
 exportMethods(sensitivityInfo)
 exportMethods(sensitivityMeasures)
+exportMethods(sensitivityProfiles)
 exportMethods(show)
-exportMethods(snpData)
-exportMethods(snpInfo)
-import(Biobase)
 import(RColorBrewer)
 import(caTools)
 import(downloader)
-import(magicaxis)
 import(methods)
 import(parallel)
+importFrom(Biobase,exprs)
+importFrom(Biobase,pData)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,pdf)
 importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(graphics,abline)
+importFrom(graphics,hist)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,par)
@@ -78,7 +72,9 @@ importFrom(piano,runGSA)
 importFrom(stats,anova)
 importFrom(stats,complete.cases)
 importFrom(stats,cor.test)
+importFrom(stats,cov.wt)
 importFrom(stats,formula)
+importFrom(stats,glm)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,na.omit)
@@ -91,6 +87,8 @@ importFrom(stats,pt)
 importFrom(stats,qnorm)
 importFrom(stats,sd)
 importFrom(stats,var)
+importFrom(utils,read.table)
 importFrom(utils,sessionInfo)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
+importFrom(utils,write.table)

R/GWC.R

@@ -1,6 +1,5 @@
 ########################
 ## Benjamin Haibe-Kains
-## All rights Reserved
 ## October 23, 2013
 ########################
 
@@ -15,37 +14,37 @@
 #'  @param method.cor \code{character} string identifying if a \code{pearson} or
 #'    \code{spearman} correlation should be used
 #'  @param ... Other passed down to internal functions
-#'  
+#'
 #' @return \code{numeric} a vector of two values, the correlation and associated p-value.
-#' 
+#'
 #' @export
-##			- 
+##			-
 ##
 ## http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient#Calculating_a_weighted_correlation
 ## http://www.mathworks.com/matlabcentral/fileexchange/20846-weighted-correlation-matrix
 ## F. Pozzi, T. Di Matteo, T. Aste, "Exponential smoothing weighted correlations", The European Physical Journal B, Vol. 85, No 6, 2012. DOI: 10.1140/epjb/e2012-20697-x
 #################################################
 
-gwc <- 
+gwc <-
 function (x1, p1, x2, p2, method.cor=c("pearson", "spearman"), nperm=1e4, ...) {
-
-	method.cor <- match.arg(method.cor)
-  ## intersection between x and y
-  ii <- intersectList(names(x1), names(p1), names(x2), names(p2))
-  if(length(ii) < 10) {
-    stop ("Less than 10 probes/genes in common between x and y")
-  }
-  x1 <- x1[ii]
-  p1 <- p1[ii]
-  x2 <- x2[ii]
-  p2 <- p2[ii]
-  ## scaled weights
-  p1 <- -log10(p1)
-  p1 <- p1 / sum(p1, na.rm=TRUE)
-  p2 <- -log10(p2)
-  p2 <- p2 / sum(p2, na.rm=TRUE)
-  w <- p1 + p2
-  ## compute genome-wide connectivity score
-  res <- corWeighted(x=x1, y=x2, w=w, method=method.cor, nperm=nperm, ...)
-	return(res)
+    
+    method.cor <- match.arg(method.cor)
+    ## intersection between x and y
+    ii <- intersectList(names(x1), names(p1), names(x2), names(p2))
+    if(length(ii) < 10) {
+        stop ("Less than 10 probes/genes in common between x and y")
+    }
+    x1 <- x1[ii]
+    p1 <- p1[ii]
+    x2 <- x2[ii]
+    p2 <- p2[ii]
+    ## scaled weights
+    p1 <- -log10(p1)
+    p1 <- p1 / sum(p1, na.rm=TRUE)
+    p2 <- -log10(p2)
+    p2 <- p2 / sum(p2, na.rm=TRUE)
+    w <- p1 + p2
+    ## compute genome-wide connectivity score
+    res <- corWeighted(x=x1, y=x2, w=w, method=method.cor, nperm=nperm, ...)
+    return(res)
 }