Oncomine_datasets_one_page_filenames_not_empty<- function(filenames,Simple=TRUE){
library("textreadr")
library("stringr")
#read the long string
if (grepl(".txt",filenames)) { oncomine=suppressWarnings(paste(readLines(filenames), collapse=" "))
}else if(grepl(".doc",filenames) | grepl(".docx",filenames)) {oncomine=read_docx(filenames)}
oncomine_not=gsub(pattern = "\t",replacement = "",x = oncomine)
step0=strsplit(x=oncomine_not,split = "<b>")
step1=step0[[1]][-1]
steplength=length(step1)
Datasets=data.frame()
if (Simple==TRUE){
for (i in 1:steplength) {
Datatype=ifelse(grepl(pattern = 'Type">DNA',x = step1[[i]]),"DNA","mRNA")
study=str_extract(string = step1[[i]], pattern = '.*</b>')
study2=sub(pattern = "</b>",replacement = "",x = study)
study.no=str_extract(string = step1[[i]],pattern = 'pDatasetInfo">\\([0-9]*')
study.no2=sub(pattern = 'pDatasetInfo">\\(',replacement = "",x = study.no)
Dataset=cbind(Datatype=Datatype,Study=study2)
Datasets=rbind(Datasets,Dataset)
}
}else{
for (i in 1:steplength) {
Datatype=ifelse(grepl(pattern = 'Type">DNA',x = step1[[i]]),"DNA","mRNA")
study=str_extract(string = step1[[i]], pattern = '.*</b>')
study2=sub(pattern = "</b>",replacement = "",x = study)
study.no=str_extract(string = step1[[i]],pattern = 'pDatasetInfo">\\([0-9]*')
study.no2=sub(pattern = 'pDatasetInfo">\\(',replacement = "",x = study.no)
comparison.group=strsplit(x=step1[[i]],split = '<div>')[[1]][-1]
comparison.item2=sub(pattern = '</div> <div class=.*',replacement = "",x = comparison.group)
comparison.p.value=str_extract(string = comparison.group,pattern = 'p = [0-9]*.[0-9E-]*')
comparison.p.value2=sub(pattern = 'p = ',replacement = "",x = comparison.p.value)
comparison.p.fd=str_extract(string = comparison.group,pattern = 'fold change = [-0-9]*.[0-9E-]*')
comparison.p.fd2=sub(pattern = 'fold change = ',replacement = "",x = comparison.p.fd)
comparison.rank=str_extract(string = comparison.group,pattern = 'pAnalysisRank">[0-9]*')
comparison.rank2=sub(pattern = 'pAnalysisRank">',replacement = "",x = comparison.rank)
Dataset=cbind(Datatype=Datatype,Study=study2,Comparison=comparison.item2,p.value=comparison.p.value2,`Fold Change`=comparison.p.fd2,`Gene Rank`=comparison.rank2)
judge=tryCatch({Datasets=rbind(Datasets,Dataset)},error=function(e){"ERROR"})
if (is.character(judge)){
message("please click the ",i,"th drop down arrow in Oncomine web, then copy data")
next
}
}
}
return(Datasets)
}
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