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 TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="\t") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.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(wordwrap).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]]
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 at r-project.org> on behalf of Spencer Brackett <spbrackett20 at saintjosephhs.com> Sent: Sunday, August 19, 2018 2:11 PM To: r-help at 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 TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="\t") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.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(wordwrap).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]] ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help R-help -- Main R Mailing List: Primary help - Homepage - SfS<https://stat.ethz.ch/mailman/listinfo/r-help> stat.ethz.ch The main R mailing list, for announcements about the development of R and the availability of new code, questions and answers about problems and solutions using R, enhancements and patches to the source code and documentation of R, comparison and compatibility with S and S-plus, and for the posting of nice examples and benchmarks. 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]]
On Sun, 19 Aug 2018, Spencer Brackett wrote:> 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.Spencer, Looks like you want to read the data into an R dataframe; I assume that's the format for geonomic data as it is for environmental data.>> load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv")Instead, try mydata <- read.csv("lgg_drug.csv", header = TRUE, stringsAsFactors = FALSE) Note: this assumes the data file has column headers. And, you can use your .txt file with the read.table() function.> 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!How much about R have you read/learned? Taking a couple of steps back might be well worth your while. Regards, Rich
The load() function is only used for binary files that R creates with the save() function. You are trying to assign the data to an object (variable) called LGG Drug. R does not allow spaces in variable names. You could try LGGDrug, LGG_Drug, or LGG.Drug. Same issue with GBM Drug. David L. Carlson Department of Anthropology Texas A&M University -----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Spencer Brackett Sent: Sunday, August 19, 2018 2:12 PM To: r-help at 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 TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="\t") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.txt",header=TRUE,sep="") Error: unexpected symbol in "GBM Drug"> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIALGBM.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(wordwrap).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]] ______________________________________________ R-help at 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.
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 On August 19, 2018 12:16:14 PM PDT, "Sparks, John" <jspark4 at 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 at r-project.org> on behalf of Spencer >Brackett <spbrackett20 at saintjosephhs.com> >Sent: Sunday, August 19, 2018 2:11 PM >To: r-help at 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]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >R-help -- Main R Mailing List: Primary help - Homepage - >SfS<https://stat.ethz.ch/mailman/listinfo/r-help> >stat.ethz.ch >The main R mailing list, for announcements about the development of R >and the availability of new code, questions and answers about problems >and solutions using R, enhancements and patches to the source code and >documentation of R, comparison and compatibility with S and S-plus, and >for the posting of nice examples and benchmarks. > > > >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]]-- Sent from my phone. Please excuse my brevity.