Nothing
## ----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)
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