[R] Request for R Assistance: Downloading Data

[Spencer Brackett]

 Please ignore my last post/inquiry... I have solved the problem. Thanks
again for the help!

On Sun, Aug 19, 2018 at 5:43 PM Sparks, John <jspark4 using uic.edu> wrote:

> 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
> >
> >        [[alternative HTML version deleted]]
> >
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> >
> >
> >
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> >and provide commented, minimal, self-contained, reproducible code.
> >
> >       [[alternative HTML version deleted]]
>
> --
> Sent from my phone. Please excuse my brevity.
>

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