[R] Request for R Assistance: Downloading Data

[Sparks, John]

Just a hunch, but I would recommend simplifying your filename:  remove the (CSV) portion.  It could be confusing in R read syntax.  Create a filename with no unnecessary punctuation and no blank spaces.


--John Sparks


________________________________
From: R-help <r-help-bounces using r-project.org> on behalf of Spencer Brackett <spbrackett20 using saintjosephhs.com>
Sent: Sunday, August 19, 2018 2:11 PM
To: r-help using r-project.org
Subject: [R] Request for R Assistance: Downloading Data

Good evening,

  I am attempting to download Genomic data from the GDC onto R for analysis
and am experiencing some difficulty. I have downloaded the GDC data into an
Excel, CSV, and notepad (.txt) file and implemented what I believe to be
the proper arguments, with every attempting failing to properly load the
data onto R. The following is the various attempts I made in trying to take
one of these files (a translated version of the GDC data) and load it into R
.

> load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv")
Error in load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") :
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file �LGG Drug (CSV).csv� has magic number 'MANIF'
  Use of save versions prior to 2 is deprecated
> LGG Drug<-read.table("C:\\Users\\Spencer\\Desktop\\LGG Drug
(CSV).csv",header=TRUE,sep=",")
Error: unexpected symbol in "LGG Drug"
> LGG Drug<-read.table("C:
Error: unexpected symbol in "LGG Drug"
> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt")
Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") :
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file �DRUG TRIAL GBM.txt� has magic number 'MANIF'
  Use of save versions prior to 2 is deprecated
> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL
GBM.txt",header=TRUE,sep="")
Error: unexpected symbol in "GBM Drug"
> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL
GBM.txt",header=TRUE,sep="\t")
Error: unexpected symbol in "GBM Drug"
> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL
GBM.txt",header=TRUE,sep="")
Error: unexpected symbol in "GBM Drug"
>  GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL
GBM.txt",header=TRUE,sep="\t")
Error: unexpected symbol in " GBM Drug"
> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word wrap).txt")
Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word wrap).txt")
:
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file �DRUG TRIAL GBM(word wrap).txt� has magic number 'MANIF'
  Use of save versions prior to 2 is deprecated
> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word
wrap).txt",header=TRUE,sep="")
Error: unexpected symbol in "GBM Drug"

Any insight into what perhaps I am inputting that is causes this
reoccurring error? Any suggestions as to another procedure for moving
forward would be greatly appreciated!

Many thanks,

Spencer Brackett

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