Nothing
createHTML <-
function(output_file_name, segmentation, pval_threshold, loss_threshold,
gain_threshold, loh_percentage, loh_threshold, baf, n_samples,
n_probes, chromosomes, beta, min_region_bp_size,
bs, getGenes, correction){
## This function generates the html file reporting the list
## (with the respective details) of each detected region
## check if BAFs are observed
if(baf==TRUE){
print_baf <- "YES"
}else{
print_baf <- "NO"
}
n_reg <- nrow(segmentation)
loss_pos <- which(as.numeric(segmentation[,6])<=pval_threshold)
n_loss <- length(loss_pos)
gain_pos <- which(as.numeric(segmentation[,7])<=pval_threshold)
n_gain <- length(gain_pos)
n_loh = "No Available"
if(baf==TRUE){
loh_pos <- which(as.numeric(segmentation[,8])<=pval_threshold)
n_loh <- length(loh_pos)
}
## Create the Header
inFile <- system.file("template/HeaderRegions.html", package="VegaMC")
inFile <- file(inFile, "r")
outFile <- file(output_file_name, "w")
html_genes=""
if(getGenes == TRUE){
html_genes <- paste(substr(output_file_name, 1,
nchar(output_file_name)-5), "Genes.html", sep="")
}
values <- c(TITLE=output_file_name, DATE=date(), GENEFILE=html_genes)
copySubstitute(inFile, outFile, values)
close(inFile)
## Create the Summary
inFile <- system.file("template/InputParameters.html",
package="VegaMC")
inFile <- file(inFile, "r")
minBP = "No"
if(is.na(min_region_bp_size)==FALSE){
minBP=paste(format(min_region_bp_size,
big.mark="."), "bp")
}
values <- c(NUMSAMPLE=format(n_samples, big.mark="."))
values <- c(values, NUMCHR=length(chromosomes))
values <- c(values, NUMPROBE=format(n_probes, big.mark="."),
BAF=print_baf)
values <- c(values, BETA=format(beta, decimal.mark=","))
values <- c(values, MINBP=minBP)
values <- c(values, LOSST=format(loss_threshold, decimal.mark=","))
values <- c(values, GAINT=format(gain_threshold, decimal.mark=","))
values <- c(values, LOHT=format(loh_threshold, decimal.mark=","))
values <- c(values, LOHP=paste(format(as.integer(loh_percentage*100),
decimal.mark=","),"%"))
values <- c(values, BS=format(bs, big.mark="."))
values <- c(values, PVAL=format(pval_threshold, scientific=TRUE))
values <- c(values, NUMREG=format(n_reg, big.mark="."))
values <- c(values, NUMDEL=format(n_loss, big.mark="."))
values <- c(values, NUMAMP=format(n_gain, big.mark="."))
if(baf==TRUE){
values <- c(values, NUMLOH=format(n_loh, big.mark="."))
}else{
values <- c(values, NUMLOH=n_loh)
}
if(correction==TRUE){
values <- c(values, SIGN="q")
}else{
values <- c(values, SIGN="p")
}
copySubstitute(inFile, outFile, values)
close(inFile)
## Create the Header for the Table of all Regions
inFile <- system.file("template/HeaderTableAllRegions.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, VAL="NO")
if(correction==TRUE){
values <- c(values, SIGN="q")
}else{
values <- c(values, SIGN="p")
}
copySubstitute(inFile, outFile, values)
close(inFile)
## Insert a new Line for each region
segmentation[,2:4] <- format(as.integer(segmentation[,2:4]),
big.mark=".")
segmentation[,c(5,13:15)] <- format(as.numeric(segmentation[,c(5,13:15)]),
decimal.mark=",")
segmentation[,6:8] <- format(round(as.numeric(segmentation[,6:8]), 5),
decimal.mark=",")
segmentation[,16:18] <- format(round(as.numeric(segmentation[,16:18]), 5),
decimal.mark=",")
for(i in 1:n_reg){
inFile <- system.file("template/AllRegionTableRow.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c()
values <- c(CHR=as.character(segmentation[i,1]))
values <- c(values, BPSTART=as.character(segmentation[i,2]))
values <- c(values, BPEND=as.character(segmentation[i,3]))
values <- c(values, BPSIZE=as.character(segmentation[i,4]))
values <- c(values, L2MEAN=as.character(segmentation[i,5]))
values <- c(values, LOSSPVAL=as.character(segmentation[i,6]))
values <- c(values, LOSSPRC=as.character(segmentation[i,9]))
values <- c(values, GAINPVAL=as.character(segmentation[i,7]))
values <- c(values, GAINPRC=as.character(segmentation[i,10]))
values <- c(values, LOHPVAL=as.character(segmentation[i,8]))
values <- c(values, LOHPRC=as.character(segmentation[i,11]))
copySubstitute(inFile, outFile, values)
close(inFile)
}
## Create the Footer for the Table of all Regions
inFile <- system.file("template/FooterTable.html", package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, VAL="NO")
copySubstitute(inFile, outFile, values)
close(inFile)
if(length(loss_pos)>0){
tmp <- segmentation[loss_pos,]
tmp <- tmp[order(as.numeric(substr(tmp[,9], 1, nchar(tmp[,9])-1)),
decreasing=TRUE),]
## Create the Header for the Table of Deleted Regions
inFile <- system.file("template/HeaderTableAberrantRegions.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, TABNAME="Deleted", ABERR="Loss")
if(correction==TRUE){
values <- c(values, SIGN="q")
}else{
values <- c(values, SIGN="p")
}
copySubstitute(inFile, outFile, values)
close(inFile)
## Insert a new Line for each region
for(i in 1:length(loss_pos)){
inFile <- system.file(
"template/AberrantRegionTableRow.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c()
values <- c(CHR=as.character(tmp[i,1]))
values <- c(values,
BPSTART=as.character(tmp[i,2]))
values <- c(values,
BPEND=as.character(tmp[i,3]))
values <- c(values,
BPSIZE=as.character(tmp[i,4]))
values <- c(values,
L2MEAN=as.character(tmp[i,13]))
values <- c(values,
ABERRPVAL=as.character(tmp[i,6]))
values <- c(values,
ABERRPRC=as.character(tmp[i,9]))
values <- c(values,
FOC=as.character(tmp[i,16]))
copySubstitute(inFile, outFile, values)
close(inFile)
}
## Create the Footer for the Table of Deleted Regions
inFile <- system.file("template/FooterTable.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, VAL="NO")
copySubstitute(inFile, outFile, values)
close(inFile)
}
if(length(gain_pos)>0){
tmp <- segmentation[gain_pos,]
tmp <- tmp[order(as.numeric(substr(tmp[,10], 1, nchar(tmp[,10])-1)),
decreasing=TRUE),]
## Create the Header for the Table of Amplified Regions
inFile <- system.file("template/HeaderTableAberrantRegions.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, TABNAME="Amplified", ABERR="Gain")
if(correction==TRUE){
values <- c(values, SIGN="q")
}else{
values <- c(values, SIGN="p")
}
copySubstitute(inFile, outFile, values)
close(inFile)
## Insert a new Line for each region
for(i in 1:length(gain_pos)){
inFile <- system.file(
"template/AberrantRegionTableRow.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c()
values <- c(CHR=as.character(tmp[i,1]))
values <- c(values,
BPSTART=as.character(tmp[i,2]))
values <- c(values,
BPEND=as.character(tmp[i,3]))
values <- c(values,
BPSIZE=as.character(tmp[i,4]))
values <- c(values,
L2MEAN=as.character(tmp[i,14]))
values <- c(values,
ABERRPVAL=as.character(tmp[i,7]))
values <- c(values,
ABERRPRC=as.character(tmp[i,10]))
values <- c(values,
FOC=as.character(tmp[i,17]))
copySubstitute(inFile, outFile, values)
close(inFile)
}
## Create the Footer for the Table of Amplified Regions
inFile <- system.file("template/FooterTable.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, VAL="NO")
copySubstitute(inFile, outFile, values)
close(inFile)
}
if(baf==TRUE){
if(length(loh_pos)>0){
tmp <- segmentation[loh_pos,]
tmp <- tmp[order(as.numeric(substr(tmp[,11], 1, nchar(tmp[,11])-1)),
decreasing=TRUE),]
inFile <- system.file(
"template/HeaderTableAberrantRegions.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, TABNAME="LOH", ABERR="LOH")
if(correction==TRUE){
values <- c(values, SIGN="q")
}else{
values <- c(values, SIGN="p")
}
copySubstitute(inFile, outFile, values)
close(inFile)
for(i in 1:length(loh_pos)){
inFile <- system.file(
"template/AberrantRegionTableRow.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c()
values <- c(CHR=as.character(tmp[i,1]))
values <- c(values,
BPSTART=as.character(tmp[i,2]))
values <- c(values,
BPEND=as.character(tmp[i,3]))
values <- c(values,
BPSIZE=as.character(tmp[i,4]))
values <- c(values,
L2MEAN=as.character(tmp[i,15]))
values <- c(values,
ABERRPVAL=as.character(tmp[i,8]))
values <- c(values,
ABERRPRC=as.character(tmp[i,11]))
values <- c(values,
FOC=as.character(tmp[i,18]))
copySubstitute(inFile, outFile, values)
close(inFile)
}
## Create the Footer for the Table of Amplified Regions
inFile <- system.file("template/FooterTable.html",
package="VegaMC")
inFile <- file(inFile, "r")
values <- c(values, VAL="NO")
copySubstitute(inFile, outFile, values)
close(inFile)
}
}
## Create the Footer
inFile <- system.file("template/Footer.html", package="VegaMC")
inFile <- file(inFile, "r")
values <- c(BIOINFO="http://bioinformatics.biogem.it")
copySubstitute(inFile, outFile, values)
close(inFile)
close(outFile)
}
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