[R] TCGA biolinks, DNA methylation

[Spencer Brackett]

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]]
>> >>
>> >> ______________________________________________
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>> >> 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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