[R] Request for R Assistance: Downloading Data

[Sparks, John]

I agree with Jeff.  The data type is the problem.  I wrote what I wrote without looking at the problem very carefully.


--JJS


________________________________
From: Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
Sent: Sunday, August 19, 2018 4:38 PM
To: r-help using r-project.org; Sparks, John; Spencer Brackett; r-help using r-project.org
Subject: Re: [R] Request for R Assistance: Downloading Data

I think this hunch is off the mark... the file name is fine as it is... if anything will confuse R it would be that the data inside the file are not what was expected.

If in fact the file is csv formatted then the function to read it would be read.csv [1] or read.table [2]. Read the help pages for these functions and read the R Data Import/Export documentation [3].

[1] ?read.csv at R console
[2] ?read.table many of the options for this function will work for read.csv.
[3] https://cran.r-project.org/doc/manuals/r-release/R-data.html
R Data Import/Export<https://cran.r-project.org/doc/manuals/r-release/R-data.html>
cran.r-project.org
1.1 Imports. The easiest form of data to import into R is a simple text file, and this will often be acceptable for problems of small or medium scale.




On August 19, 2018 12:16:14 PM PDT, "Sparks, John" <jspark4 using uic.edu> wrote:
>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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--
Sent from my phone. Please excuse my brevity.

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