[R] TCGA biolinks, DNA methylation

[Spencer Brackett]

  Thank you! The line however was still found to be errored after I fixed
the mistake. Is there anything else I can do to maybe set the “.” As an
object?

Spencer

On Wed, Aug 29, 2018 at 6:34 PM Sarah Goslee <sarah.goslee using gmail.com> wrote:

> Hi,
>
> If you had an actual gene analysis question I'd suggest the
> BioConductor email list, but you have a plain old ordinary typo:
>
>  the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",")
>
> You're missing the = after the argument sep
>
>  the_data <- read.csv(file = "LGG_clinical_drug.csv", header = TRUE, sep =
> ",")
>
> Using more spaces in your code would make that typo easier to spot.
>
> Sarah
> On Wed, Aug 29, 2018 at 6:06 PM 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
> >
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>

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