[R] Problems w/ creating object

William Dunlap wdun|@p @end|ng |rom t|bco@com
Mon Apr 22 23:24:37 CEST 2019 

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 <wdunlap using 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 <dwinsemius using 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 using 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 using 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.
>>
>

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