#' To clear Oncomine data for Clinical Outcome data
#'
#' @param filenames The filenames that your data stored in. if ONLY data files in your working directory this object can be omitted.
#' @param NoValue a logistic value
#' @return a dataframe
#' @export
#'
#' @examples Oncomine_ClinicalOutcome()
Oncomine_ClinicalOutcome<-function(filenames,NoValue=TRUE){
if (missing(filenames)){
filenames=list.files()
}
txtcheck=filenames[grepl(pattern = ".txt",x = filenames)==FALSE]
docxcheck=txtcheck[grepl(pattern = ".docx",x = txtcheck)==FALSE]
doccheck=docxcheck[grepl(pattern = ".doc",x = docxcheck)==FALSE]
if (length(doccheck)==0){
survival.i=data.frame()
for ( i in 1:length(filenames)){
ONAME=sub(pattern = "\\..*",replacement = "",x = filenames[i])
if (i==1){
Osurvival.1=Oncomine_bar(filenames[i])
if (NoValue==FALSE){
survival.i=Osurvival.1[!(Osurvival.1$`Legend Value`=="No value"),]
}else if (NoValue==TRUE){
survival.i=Osurvival.1
}
colnames(survival.i)[grep(pattern = "Legend Value",x = colnames(survival.i))]=ONAME
}else if (i>1){
Osurvival.i=Oncomine_bar(filenames[i])
if (NoValue==FALSE){
Osurvival.i2=Osurvival.i[!(Osurvival.i$`Legend Value`=="No value"),]
}else if(NoValue==TRUE){
Osurvival.i2=Osurvival.i
}
Osurvival.i4=Osurvival.i2[,c(grep(pattern = "Sample Name",x = colnames(Osurvival.i2)),
grep(pattern = "Legend Value",x = colnames(Osurvival.i2)))]
colnames(Osurvival.i4)[grep("Legend Value",colnames(Osurvival.i4))]=ONAME
survival.i=merge(survival.i,Osurvival.i4,"Sample Name")
}
}
return(survival.i)
}else{
doccheck1=paste(doccheck,collapse="\n")
warning("The following files shoul be removed","\n",doccheck1)
stop("Please make sure ONLY data file end with .txt .doc .docx including in the working directory. Or give object to this function")
}
}
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