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### R code from vignette source 'gettingPbcmcData.Rnw'
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### code chunk number 1: gettingData (eval = FALSE)
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## library(limma);
## library(pbcmc);
##
## # datasets included in BioConductor repository
## libNames <- c("mainz", "nki", "transbig", "unt", "upp", "vdx");
##
## # let's load them!
## pbcmcData <- lapply(libNames, function(actLibName) {
## print(actLibName);
##
## # the pbcmc package provides an easy way to download and classify them
## actLib <- loadBCDataset(Class=PAM50, libname=actLibName, verbose=FALSE);
## actLibFilt <- filtrate(actLib, verbose=FALSE);
## actLibFilt <- classify(actLibFilt, std="none", verbose=FALSE);
## actSubtypes <- classification(actLibFilt)$subtype;
##
## # get the expression matrix and the annotation
## actExprs <- exprs(actLib);
## actAnnot <- annotation(actLib);
##
## # we recommend working allways with Entrez IDs, let's match them with
## # expression matrix rownames (and modify them)
## if (all(actAnnot$probe == rownames(actExprs))) {
## actExprs <- actExprs[!is.na(actAnnot$EntrezGene.ID),];
## actAnnot <- actAnnot[!is.na(actAnnot$EntrezGene.ID),];
## rownames(actExprs) <- as.character(actAnnot$EntrezGene.ID);
## } else {
## matchedEntrez <- match(rownames(actExprs), actAnnot$probe);
## # all(rownames(actExprs) %in% actAnnot$probe == !is.na(matchedEntrez));
##
## stopifnot(all(
## actAnnot$probe[!is.na(matchedEntrez)] ==
## rownames(actExprs)[!is.na(matchedEntrez)]));
##
## actExprs <- actExprs[!is.na(matchedEntrez),];
## actAnnot <- actAnnot[!is.na(matchedEntrez),];
## stopifnot(all(actAnnot$probe == rownames(actExprs)));
## actExprs <- actExprs[!is.na(actAnnot$EntrezGene.ID),];
## actAnnot <- actAnnot[!is.na(actAnnot$EntrezGene.ID),];
## rownames(actExprs) <- as.character(actAnnot$EntrezGene.ID);
## }
##
## # average repeated genes expression
## actExprs <- avereps(actExprs);
##
## stopifnot(all(colnames(actExprs) == names(actSubtypes)));
## # filtrate only these two conditions
## actExprs <- actExprs[, actSubtypes %in% c("Basal", "LumA")];
## actSubtypes <- as.character(
## actSubtypes[actSubtypes %in% c("Basal", "LumA")]);
##
## return(list(geneExpr=actExprs, subtypes=actSubtypes));
## })
## names(pbcmcData) <- libNames;
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### code chunk number 2: validateData (eval = FALSE)
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## # save the just created pbcmcData to newPbcmcData
## newPbcmcData <- pbcmcData;
##
## library(MIGSAdata);
##
## # and load the MIGSAdata one.
## data(pbcmcData);
## all.equal(newPbcmcData, pbcmcData);
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### code chunk number 3: Session Info
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sessionInfo()
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