Also, recall that on Windows each drive has its own root directory so the meaning of "/some/file" depends on where your working directory is at the moment. E.g.,
> setwd("C:/tmp") > cat(file="junk.txt",1:10) > file.info("/tmp/junk.txt") size isdir mode mtime ctime atime exe /tmp/junk.txt 20 FALSE 666 2019-04-22 14:20:06 2018-05-15 09:38:02 2018-05-15 09:38:02 no > setwd("Z:/") # I've mapped Z: to a network location > file.info("/tmp/junk.txt") size isdir mode mtime ctime atime exe /tmp/junk.txt NA NA <NA> <NA> <NA> <NA> <NA> > file.info("C:/tmp/junk.txt") # add drive-colon to file name size isdir mode mtime ctime atime exe C:/tmp/junk.txt 20 FALSE 666 2019-04-22 14:20:06 2018-05-15 09:38:02 2018-05-15 09:38:02 no Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Apr 22, 2019 at 2:09 PM William Dunlap <wdun...@tibco.com> wrote: > file.info( > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt" ) > would tell about the permissions on the file, if it exists (and give NA's > if it did not). > > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > > On Mon, Apr 22, 2019 at 2:00 PM David Winsemius <dwinsem...@comcast.net> > wrote: > >> >> On 4/22/19 11:49 AM, Spencer Brackett wrote: >> > Hello R users, >> > >> > I am trying to create an object out of some data a colleague sent my >> way, >> > so to duplicate the following code... >> > >> > library(data.table) >> > anno = as.data.frame(fread(file = >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", sep >> ="\t", >> > header = T)) >> >> >> At first glance it appeared that you sent the list a rather extensive >> bit of code and asked us to figure something out, but after looking at >> the error message it instead appears the it was the first effort at >> reading data from disk that threw an error. So the rest of the code is >> at best unnecessary and at worst seriously distracting (to us and more >> crucially to you). >> >> You should run your code one line at a time so you and the rest of us >> are not completely distracted. This was the error message: >> >> > anno = as.data.frame(fread(file = >> >> "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", sep ="\t", >> header = T)) >> Error in fread(file = >> "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", : >> File '/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt' does >> not exist or is non-readable. >> >> You claim this file exists, but I'm uncertain how convincing that >> assertion should be "scored". What do either of these show? >> >> list.files(pattern =".txt$") >> >> # Or >> >> "mapper.txt" %in% list.files( paste0 ( getwd(), >> "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K")) >> >> -- >> >> David. >> >> >> PS Please learn to post in plain-text. It didn't cause a problem this >> time but it probably will at some time in the future. >> >> > meth = read.table(file = >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/27K/GBM.txt", sep ="\t", >> > header = T, row.names = 1) >> > meth = as.matrix(meth) >> > """ the loop just formats the methylation column names to match >> format""" >> > colnames(meth) = sapply(colnames(meth), function(i){ >> > c1 = strsplit(i,split = '.', fixed = T)[[1]] >> > c1[4] = paste(strsplit(c1[4],split = "",fixed = >> T)[[1]][1:2],collapse = >> > "") >> > paste(c1,collapse = ".") >> > }) >> > exp = read.table(file = >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/RNAseq/GBM.txt", sep = >> "\t", >> > header = T, row.names = 1) >> > exp = as.matrix(exp) >> > c = intersect(colnames(exp),colnames(meth)) >> > exp = exp[,c] >> > meth = meth[,c] >> > m = apply(meth, 1, function(i){ >> > log2(i/(1-i)) >> > }) >> > m = t(as.matrix(m)) >> > an = anno[anno$probe %in% rownames(m),] >> > an = an[an$gene %in% rownames(exp),] >> > an = an[an$location %in% c("TSS200","TSS1500"),] >> > >> > p = apply(an,1,function(i){ >> > tryCatch(summary(lm(exp[as.character(i[2]),] ~ >> > m[as.character(i[1]),]))$coefficient[2,4], error= function(e)NA) >> > }) >> > t = apply(an,1,function(i){ >> > tryCatch(summary(lm(exp[as.character(i[2]),] ~ >> > m[as.character(i[1]),]))$coefficient[2,3], error= function(e)NA) >> > }) >> > an1 =cbind(an,p) >> > an1 = cbind(an1,t) >> > an1$q = p.adjust(as.numeric(an1$p)) >> > summary(lm(exp["MAOB",] ~ m["cg00121904",]$coefficient[2,c(3:4)] >> > ############################################### >> > >> > m2 = m >> > ll = list() >> > for(i in colnames(m2)){ >> > str = strsplit(i, split = ".", fixed = T)[[1]] >> > if(str[4] == "11"){ >> > >> > }else{ >> > ll = c(ll,i) >> > } >> > } >> > ll = unlist(ll) >> > m2 = m2[,ll] >> > colnames(m2) = sapply(colnames(m2), function(i){ >> > str = strsplit(i,split = ".", fixed = T)[[1]] >> > p = paste(str[c(1:3)], collapse = "-") >> > }) >> > >> > >> > clin = as.data.frame(fread(file = >> > >> "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/survival/FireHose/GBM/GBM.clin.merged.txt", >> > sep = "\t", header = F)) >> > clin = t(clin) >> > colnames(clin) = clin[1,] >> > rownames(clin) = toupper(clin[,"patient.bcr_patient_barcode"]) >> > clin = clin[2:length(clin[,1]),] >> > #"patient.stage_event.pathologic_stage" >> > clin1 = >> > >> clin[,c("patient.age_at_initial_pathologic_diagnosis","patient.days_to_death","patient.days_to_last_followup","patient.vital_status")] >> > clin1 = cbind(clin1,rep("bla",length(clin1[,1]))) >> > clin2 = as.matrix(clin1) >> > colnames(clin2)[length(colnames(clin2))] = "time" >> > >> > for(i in rownames(clin2)){ >> > >> > if(clin2[i,"patient.vital_status"] %in% c("alive")){ >> > clin2[i,"patient.vital_status"] =0 >> > }else if(clin2[i,"patient.vital_status"] %in% c("dead")){ >> > clin2[i,"patient.vital_status"] =1 >> > }else{ >> > clin2[i,"patient.vital_status"] = "NA" >> > } >> > >> > if(is.na(clin2[i,"patient.days_to_last_followup"])){ >> > clin2[i,"time"] = clin2[i,"patient.days_to_death"] >> > }else{ >> > clin2[i,"time"] = clin2[i,"patient.days_to_last_followup"] >> > } >> > } >> > >> > clin2 = clin2[!is.na(clin2[,"time"]),] >> > clin2 = clin2[!is.na(clin2[,"patient.vital_status"]),] >> > >> > library(survival) >> > p = intersect(colnames(m2), rownames(clin2)) >> > surv = >> > >> Surv(as.numeric(clin2[p,"time"]),as.numeric(clin2[p,"patient.vital_status"])) >> > >> > an_m = anno[anno$probe %in% rownames(m2),] >> > an_m = an[an$gene %in% rownames(exp),] >> > >> > sur_z = apply(an_m, 1, function(i){ >> > tryCatch(summary(coxph(surv ~ >> > >> as.numeric(m2[as.character(i[1]),p])+as.numeric(clin2[p,"patient.age_at_initial_pathologic_diagnosis"])))$coefficients[1,c("z")], >> > error = function(e) NA) >> > }) >> > >> > sur_p = apply(an_m, 1, function(i){ >> > tryCatch(summary(coxph(surv ~ >> > >> as.numeric(m2[as.character(i[1]),p])+as.numeric(clin2[p,"patient.age_at_initial_pathologic_diagnosis"])))$coefficients[1,c("Pr(>|z|)")], >> > error = function(e) NA) >> > }) >> > >> > qsur = p.adjust(as.numeric(sur_p)) >> > sur = cbind(sur_z,sur_p) >> > sur = cbind(sur,qsur) >> > >> > >> > The file is a text file >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", which is >> > then proceeded by another txt. file >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/27K/GBM.txt, which I wish >> to >> > load subsequently. However, when i tried copying the procedure above I >> > received the following error message.. >> > >> > library(data.table) >> >> anno = as.data.frame(fread(file = >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", sep >> ="\t", >> > header = T)) >> > Error in fread(file = >> > "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", : >> > File '/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt' >> does >> > not exist or is non-readable. >> > getwd()=='C:/Users/Spencer/Documents' >> > >> > The file does exit so in what context is it 'unreadable' and how might I >> > solve this situation? >> > >> > Best, >> > >> > Spencer >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help >> > PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> > and provide commented, minimal, self-contained, reproducible code. >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.