SHYABI
哪位大佬可以帮我看看这个代码不 一直在报错 debug之后提示不是所有的"check the url1"都是TURE 还有就是 download.file(url1,destfile = downfile)里面url参数不对
Downld_xena<-function(url1=NULL,outname="download.txt",destdir="./",datatype="rna",clean=T,RMraw=T){
if(!require(dplyr)){
install.packages("dplyr")
}
if(!require(tibble)){
install.packages("tibble")
}
if (!datatype %in% c("rna","clinical","survival")) {
stopifnot("datatype must be rna clinical or survival")
}
if(is.null(url1) | !is.character(url1)){
stopifnot("check the url1")
}
downfile<-paste(destdir="./",rev(strsplit(rna_url,"/")[[1]])[1],sep = "/")
download.file(url1,destfile = downfile)
downdata<-data.table::fread(downfile)
if(datatype=="clinical"&clean){
downdata<-downdata %>%
dplyr::rename(Age=age_at_inital_pathologic_diagnosis,
Gender=gender.demographic,
PID=submitter.id,
Sample_ID=submitter.id.samples,
Sample=sample_type.samples,
Stage=tumor_stage.diagnoses,
Mstage=pathologic_M,
Tstage=pathologic_T,
Nstage=pathologic_N) %>%
dplyr::select(-c(starts_with("additional"),starts_with("year"),
starts_with("bcr"),starts_with("pathology"),
starts_with("days"),starts_with("age",ignore.case = F)))%>%
dplyr::select(PID,Sample_ID,Sample_Type,Age,Gender,Stage,Tstage,Nstage,Mstage,everything())
downdata[downdata==""]<-NA
}else{
downdata<-tibble::column_to_rownames(var = "Ensembl_ID")
}
if(datatype=="survival"&clean){
downdata<-downdata %>%
dplyr::rename(OS.status=OS,OS=OS.time)
}
saveRDS(downdata,paste(destdir,outname,sep = "/"))
cat("File has downloaded and stored",destdir,"\n")
if(RMraw){
file.remove(downfile)
}
}
rna_url<-"https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-CHOL.htseq_counts.tsv.gz"
Downld_xena(url1=rna_url,outname = "Bileductcancer_rna.RDS",destdir = "./Readfiles/",datatype = "rna")
traceback()
debug(Downld_xena)
Downld_xena()
dxyc42u
有时候是软件本身的问题,可以试下卸载了重新安装
土井挞克树
这个需要下载个函数包,之后就不会报错了。