[R] Help converting .txt to .csv file

PIKAL Petr petr@pik@l @ending from prechez@@cz
Thu Dec 27 09:27:50 CET 2018


Hi

See inline

> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Spencer Brackett
> Sent: Thursday, December 27, 2018 3:57 AM
> To: Richard M. Heiberger <rmh using temple.edu>
> Cc: R-help <r-help using r-project.org>
> Subject: Re: [R] Help converting .txt to .csv file
>
> Hello again,
>
> I worked on directly downloading the file into R as was suggested, but have
> thus far been unsuccessful. This is what  I generated on my second attempt...
>
>  GBM protein_expression<-(file.choose(), header=TRUE, sep="\t")
> Error: unexpected symbol in "GBM protein_expression"
> > GBM

You forgot to add read.* function.

something like
protein_expression <- read.delim(file.choose())

or

protein_expression <- read.table(file.choose(), header=TRUE, sep="\t")

If your files are tab delimited as Richard suggested.

Cheers
Petr

> protein_expression<-(file.choose(GBM_protein_expression.xlsx),header=TRUE,
> sep="\t")
> Error: unexpected symbol in "GBM protein_expression"
> >
>
> What part of the argument is in error?
>
> Also I tried importing the dataset as an excel file on RStudio to see if I could
> solve my problem that way. However, my imported excel file has been stuck in
> the 'retrieving preview data' and no data is appearing. Is the data file prehaps
> too large or in the wrong format?
>
>
>
> On Wed, Dec 26, 2018 at 6:42 PM Spencer Brackett <
> spbrackett20 using saintjosephhs.com> wrote:
>
> > Mr. Heiberger,
> >
> >  Thank you for the insight! I will try out suggestion.
> >
> > Best,
> >
> > Spencer Brackett
> >
> > On Wed, Dec 26, 2018 at 6:34 PM Richard M. Heiberger <rmh using temple.edu>
> > wrote:
> >
> >> I looked at the first file.  It gives an option to download as TSV
> >> (tab separated values).
> >> That is the same as CSV except with tabs instead of commas.
> >> You do not need any external software to read it.  Read the
> >> downloaded file directly into R.
> >>
> >> read.delim looks as if it would work directly on the downloaded file.
> >> ?read.delim
> >> The notation "\t" means the tab character.
> >>
> >> As an aside, stay away from notepad. it is too naive for almost
> >> anything interesting.
> >> The specific case I often see is people reading linux-style text
> >> files with notepad, which doesn't understand NL terminated lines.
> >> nicely formatted text files become illegible.
> >>
> >> On Wed, Dec 26, 2018 at 6:04 PM Spencer Brackett
> >> <spbrackett20 using saintjosephhs.com> wrote:
> >> >
> >> > Good evening,
> >> >
> >> > I am attempting to anaylze the protein expression data contained
> >> > within these two ICGC, TCGA datasets (one for GBM and the other for
> >> > LGG)
> >> >
> >> > *File for GBM  protein expression*:
> >> >
> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22
> >> :%7B%22is%22:%5B%22GBM-
> US%22%5D%7D,%22availableDataTypes%22:%7B%22is%
> >> 22:%5B%22pexp%22%5D%7D%7D%7D
> >> >
> >> > *File for LGG protein expression:*
> >> >
> >> >
> >> > *
> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22
> >> :%7B%22is%22:%5B%22LGG-
> US%22%5D%7D,%22availableDataTypes%22:%7B%22is%
> >> 22:%5B%22pexp%22%5D%7D%7D%7D
> >> > <
> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22
> >> :%7B%22is%22:%5B%22LGG-
> US%22%5D%7D,%22availableDataTypes%22:%7B%22is%
> >> 22:%5B%22pexp%22%5D%7D%7D%7D
> >> >*
> >> >
> >> >   When I tried to transfer the files from .txt (via Notepad) to
> >> > .csv
> >> (via
> >> > Excel), the data appeared in the columns as unorganized and random
> >> > script... not like how a typical csv should be arranged at all. I
> >> > need
> >> the
> >> > dataset to be converted into .csv in order to analyze it in R,
> >> > which is
> >> why
> >> > I am hoping someone here might help me in doing that. If not, is
> >> > there perhaps some other way that I could analyze the datatsets on
> >> > R, which
> >> again
> >> > is downloaded from the dataportal ICGC?
> >> >
> >> > Best,
> >> >
> >> > Spencer Brackett
> >> >
> >> >         [[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.
> >>
> >
>
> [[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.
Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních partnerů PRECHEZA a.s. jsou zveřejněny na: https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about processing and protection of business partner’s personal data are available on website: https://www.precheza.cz/en/personal-data-protection-principles/
Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a podléhají tomuto právně závaznému prohláąení o vyloučení odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any documents attached to it may be confidential and are subject to the legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/



More information about the R-help mailing list