[R] TCGA biolinks, DNA methylation

[Sarah Goslee]

On Wed, Aug 29, 2018 at 6:58 PM Spencer Brackett
<spbrackett20 using saintjosephhs.com> wrote:
>
>   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?

But presumably with a different error, which you don't tell us.

The "." doesn't appear anywhere in the read.csv() command that you
initially reported an error in.
All a path of "." means is "look in the current directory." So later
in your download commands, files should be saved to the current
working directory. But that doesn't have anything to do with your
current csv file.

What does

getwd()

tell you? If it is NOT the same directory that contains
LGG_clinical_drug.csv then you need to tell read.csv() where to look
for it.

the_data <- read.csv(file = "path/to/file/LGG_clinical_drug.csv",
header = TRUE, sep = ",")

with whatever the actual path is.

If that's NOT the problem, or it still doesn't work, you'll need to
tell us more information. Like what the error message is, what getwd()
returns, and where the file actually is on your system.

The read.csv() commands don't seem to have anything at all to do with
the remaining part of the sample analysis you're trying to run


> 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