[R] TCGA biolinks, DNA methylation

[William Dunlap]

Try adding fileEncoding="UTF-16" to your read.csv() call.  Many Windows
programs write UTF-16 files by default.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Aug 30, 2018 at 6:05 PM, Spencer Brackett <
spbrackett20 using saintjosephhs.com> wrote:

> My apologies... the following is what I received from the correction
>
>  the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",")
> Warning messages:
> 1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   line 3 appears to contain embedded nulls
> 2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   line 4 appears to contain embedded nulls
> 3: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   line 5 appears to contain embedded nulls
> 4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
> :
>   embedded nul(s) found in input
> >
>
>
> On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry using alaska.edu> wrote:
>
> > You still haven't fixed the first thing both Sarah and I pointed out. You
> > are lacking an = between sep and ","
> >
> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",")
> >
> > should be
> >
> > the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, *sep
> > = ","*)
> >
> > as Sarah pointed out, you should use spaces to help make these errors
> more
> > obvious.
> >
> > On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett <
> > spbrackett20 using saintjosephhs.com> wrote:
> >
> >> Hello again,
> >>
> >> My apologies for the delayed response... computer troubles. In reference
> >> to
> >> Ms. Goslee's and Mr. Barry's query, the following is the error code
> >> received after I inputted my R command
> >>
> >>  the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",")
> >> Error: unexpected string constant in
> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",""
> >>
> >> Given this, should I proceed with implementing the path<getwd() ,since I
> >> am, as he suggested trying to set the variable *path* to my working
> >> directory with path<-"."
> >>
> >> Mr. Mittal also recommended importing with r studio, which I shall try
> in
> >> the meantime.
> >>
> >> Many thanks,
> >>
> >> Spencer Brackett
> >>
> >>
> >> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal <
> prof.amit.mittal using gmail.com>
> >> wrote:
> >>
> >> > Use r studio and import from the menu. Read_csv has changed
> >> >
> >> > Also you can see any format problems
> >> >
> >> > On Thu, 30 Aug 2018 3:36 am Spencer Brackett, <
> >> > spbrackett20 using saintjosephhs.com> wrote:
> >> >
> >> >> Good evening R users,
> >> >>
> >> >>   I am attempting to carry out DNA methylation analysis on two
> separate
> >> >> CSV
> >> >> files (LGG and GBM), which I have downloaded onto my R console. To
> set
> >> the
> >> >> path<-"." to be indicative of one or both of the csv files, I
> utilized
> >> the
> >> >> following functions and received the errors shown. How do I set the
> >> "." so
> >> >> that I can begin analysis on my files?
> >> >>
> >> >> > the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",")
> >> >> Error: unexpected string constant in "the_data
> >> >> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",""
> >> >> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",")
> >> >> Error: unexpected string constant in
> >> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",""
> >> >>
> >> >> This is the preliminary portion of the analysis I am trying to run,
> >> which
> >> >> I
> >> >> am referring to:
> >> >>
> >> >> 1 library(TCGAbiolinks)
> >> >> 2
> >> >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and
> GBM.
> >> >> 4 path <– "."
> >> >> 5
> >> >> 6 query.met <– TCGAquery(tumor = c("LGG","GBM"),"
> HumanMethylation450",
> >> >> level = 3)
> >> >> 7 TCGAdownload(query.met, path = path )
> >> >> 8 met <– TCGAprepare(query = query.met,dir = path,
> >> >> 9                      add.subtype = TRUE, add.clinical = TRUE,
> >> >> 10                    summarizedExperiment = TRUE,
> >> >> 11                      save = TRUE, filename = "lgg_gbm_met.rda")
> >> >> 12
> >> >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and
> GBM.
> >> >> 14 query.exp <– TCGAquery(tumor = c("lgg","gbm"), platform =
> >> >> "IlluminaHiSeq_
> >> >> RNASeqV2",level = 3)
> >> >> 15
> >> >> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_
> >> >> results")
> >> >> 17
> >> >> 18 exp <– TCGAprepare(query = query.exp, dir = path,
> >> >> 19                    summarizedExperiment = TRUE,
> >> >> 20                      add.subtype = TRUE, add.clinical = TRUE,
> >> >> 21                    type = "rsem.genes.normalized_results",
> >> >> 22                      save = T,filename = "lgg_gbm_exp.rda")
> >> >>
> >> >> Many thanks,
> >> >>
> >> >> 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.
> >>
> >
> >
>
>         [[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.
>

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