[R] TCGA biolinks, DNA methylation

[Spencer Brackett]

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

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