[R] TCGA biolinks, DNA methylation

[Spencer Brackett]

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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