## ----setup, include=FALSE, cache=FALSE, echo=FALSE---------------------------- Sys.setenv(TEXINPUTS=getwd(), BIBINPUTS=getwd(), BSTINPUTS=getwd()) ## ----setup2, include=TRUE, message=FALSE, warning=FALSE----------------------- #if (!requireNamespace("BiocManager", quietly=TRUE)) #install.packages("BiocManager") #BiocManager::install("CINdex") library(CINdex) ## ----------------------------------------------------------------------------- data("grl.data") ## ----------------------------------------------------------------------------- # loading the example file data("cnvgr.18.auto") data("snpgr.18.auto") ## ----------------------------------------------------------------------------- # loading the example file data("hg18.ucsctrack") ## ----------------------------------------------------------------------------- data("clin.crc") ## ----chrcin, eval=FALSE, warning=FALSE---------------------------------------- # run.cin.chr(grl.seg = grl.data) ## ----eval = FALSE------------------------------------------------------------- # dataMatrix_2.5_1.5_normalized_sum.RData # #gain threshold=2.5, loss threshold=1.5,normalized, showing sum (gains and losses) # # dataMatrix_2.5_1.5_unnormalized_sum.RData # #gain threshold=2.5, loss threshold=1.5, unnormalized,showing sum (gains and losses) # # dataMatrix_2.5_1.5_normalized_amp.RData # #gain threshold=2.5, loss threshold=1.5, normalized, showing amplifications # # dataMatrix_2.5_1.5_unnormalized_amp.RData # #gain threshold=2.5, loss threshold=1.5, unnormalized, showing amplifications # # dataMatrix_2.5_1.5_normalized_del.RData # #gain threshold=2.5, loss threshold=1.5, normalized, showing deletions # # dataMatrix_2.5_1.5_unnormalized_del.RData # # gain threshold=2.5, loss threshold=1.5, unnormalized,showing deletions # # dataMatrix_2.25_1.75_normalized_sum.RData # dataMatrix_2.25_1.75_unnormalized_sum.RData # dataMatrix_2.25_1.75_normalized_amp.RData # dataMatrix_2.25_1.75_unnormalized_amp.RData # dataMatrix_2.25_1.75_normalized_del.RData # dataMatrix_2.25_1.75_unnormalized_del.RData # dataMatrix_2.1_1.9_normalized_sum.RData # dataMatrix_2.1_1.9_unnormalized_sum.RData # dataMatrix_2.1_1.9_normalized_amp.RData # dataMatrix_2.1_1.9_unnormalized_amp.RData # dataMatrix_2.1_1.9_normalized_del.RData # dataMatrix_2.1_1.9_unnormalized_del.RData ## ----chrcinoneset, message = FALSE,warning=FALSE------------------------------ run.cin.chr(grl.seg = grl.data, thr.gain=2.25, thr.loss=1.75, V.def=3, V.mode="sum") ## ----cytobandcin, eval=FALSE, message = FALSE, warning=FALSE------------------ # run.cin.cyto(grl.seg = grl.data, cnvgr=cnvgr.18.auto, snpgr=snpgr.18.auto, # genome.ucsc = hg18.ucsctrack) ## ----cytoCinOneSet, warning=FALSE, results='hide'----------------------------- run.cin.cyto(grl.seg = grl.data, cnvgr=cnvgr.18.auto, snpgr=snpgr.18.auto, genome.ucsc = hg18.ucsctrack,thr.gain = 2.25,thr.loss = 1.75, V.def = 3, V.mode="sum") ## ----chrheatmap, eval=FALSE, warning=FALSE, message = FALSE------------------- # comp.heatmap(R_or_C="Regular", clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, # in.folder.name="output_chr_cin", out.folder.name="output_chr_plots") ## ----chrheatmapOneSet, warning=FALSE, message = FALSE------------------------- comp.heatmap(R_or_C="Regular", clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, thr.gain = 2.25, thr.loss = 1.75,V.def = 3,V.mode = "sum") ## ----cytoheatmap, eval=FALSE, warning=FALSE, message = FALSE,results="hide"---- # comp.heatmap(R_or_C="Cytobands", clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, # in.folder.name="output_cyto_cin", out.folder.name="output_cyto_plots") ## ----cytoHeatmapOneSet, warning=FALSE, message=FALSE, results='hide'---------- comp.heatmap(R_or_C="Cytobands", clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, in.folder.name="output_cyto_cin", out.folder.name="output_cyto_plots", thr.gain=2.25, thr.loss=1.75,V.def=3,V.mode='sum') ## ----echo=FALSE, message=FALSE, results='hide'-------------------------------- file.copy(from ="output_cyto_plots/2.25_1.75_unnormalized_sum/chr_20_dataMatrix_2.25_1.75_unnormalized_sum.png",to = "output_cyto_plots/chr20.png") ## ----eval=FALSE--------------------------------------------------------------- # load('output_cyto_cin/cytobands.cin_2.25_1.75_unnormalized_sum.RData') ## ----label=loadcytocin, echo=FALSE, warning=FALSE, message=FALSE-------------- #temp1 <- system.file("extdata", "cytobands.cin_2.25_1.75_unnormalized_sum.RData", #package = "CINdex") #load(file=temp1) data("cytobands.cin") ## ----ttest, message=FALSE, warning=FALSE,results='hide'----------------------- ttest.cyto.cin.heatmap(cytobands.cin.obj = cytobands.cin, clinical.inf = clin.crc, genome.ucsc = hg18.ucsctrack, file.ext='unnormalized') ## ----------------------------------------------------------------------------- #Loading the data into the workspace data("geneAnno") ## ----eval=FALSE--------------------------------------------------------------- # #Loading the heatmap object into the workspace # load('output_ttest/cyto.cin4heatmap.unnormalized.RData') # #object loaded is called "cyto.cin4heatmap" ## ----label=loadcyto4heatmap, echo=FALSE, warning=FALSE------------------------ data("cyto.cin4heatmap") ## ----extractgeneincyto-------------------------------------------------------- extract.genes.in.cyto.regions(cyto.cin4heatmapObj = cyto.cin4heatmap, genome.ucsc=hg18.ucsctrack, gene.annotations = geneAnno) ## ----------------------------------------------------------------------------- load("output_genename/cytoband_genes.Rdata") ## ----------------------------------------------------------------------------- inputGenes <- unique(cytoband_genes[,"geneNames"]) ## ----message=FALSE, eval=FALSE------------------------------------------------ # #Loading the package # #if (!requireNamespace("BiocManager", quietly=TRUE)) # #install.packages("BiocManager") # #BiocManager::install("org.Hs.eg.db") # library(org.Hs.eg.db) # ###### # entrez <- mapIds(x = org.Hs.eg.db,keys = inputGenes, keytype = "SYMBOL", # column = "ENTREZID") # entrez <- na.omit(entrez) ## ----message=FALSE, eval=FALSE, y=TRUE---------------------------------------- # #Loading the package # #BiocManager::install("ReactomePA") # library(ReactomePA) # # #Calling function to perform enrichment # enrich <- enrichPathway(gene = entrez, pvalueCutoff = 0.05, readable = TRUE) # #Examining and saving the results # head(enrich@result,5) # #viewing top pathway names # head(enrich@result$Description,15) # #viewing top pathway names and its p-value # head(cbind(enrich@result$Description,enrich@result$pvalue),15) # #results not displayed in this document due to its large size ## ----eval=FALSE--------------------------------------------------------------- # #saving results into a file for easy viewing # write.csv(enrich@result, "enrichment.csv",row.names = FALSE) ## ----barplots,fig.height=4, fig.width=12,eval=FALSE--------------------------- # #View results as a bar plot # barplot(enrich, showCategory=8)