[R] TCGA biolinks, DNA methylation

[Sarah Goslee]

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