[R] 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?

  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.