Problems w/ creating object

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Problems w/ creating object

Spencer Brackett
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))
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]]

______________________________________________
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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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Re: Problems w/ creating object

David Winsemius

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?

 ┬álist.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]]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: Problems w/ creating object

R help mailing list-2
  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 <[hidden email]>
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]]
> >
> > ______________________________________________
> > [hidden email] 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.
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Problems w/ creating object

R help mailing list-2
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 <[hidden email]> 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 <[hidden email]>
> 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]]
>> >
>> > ______________________________________________
>> > [hidden email] 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.
>>
>> ______________________________________________
>> [hidden email] 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]]

______________________________________________
[hidden email] 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.