Hi, I'm analyzing TCGA CNV data, following the workflow in TCGAWorkflow(https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#genomic_analysis), I write code as following to get TCGA-LIHC' CNV data:
#Genomic analysis
query.lihc.nocnv <-GDCquery(project = "TCGA-LIHC",
data.category = "Copy number variation",
legacy = TRUE,
file.type = "nocnv_hg19.seg",
sample.type = c("Primary solid Tumor"))
GDCdownload(query.lihc.nocnv)
lihc.nocnv <- GDCprepare(query.lihc.nocnv, save = TRUE, save.filename = "lihcnocnvhg19.rda")
And then, R informs me like this:
Reading copy number variation files
|===============================================================| 100%
Saving file:lihcnocnvhg19.rda
It seems s that my codes work well. However, when I read data which have been saved in the above code,data(lihcnocnvhg19), I get a Warning message:
In data(lihcnocnvhg19) : Without‘lihcnocnvhg19’dataset.
Sorry for my poor analysis experience, maybe there are some helpful person can point my faulty? Thanks very much!!
•
written
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BioLite •
1 answer
Hello,
You just have to do this:
load("lihcnocnvhg19.rda")
Kevin
Hey, where are the quotation marks in your code? Try this:
load("lihcnocnvhg19.rda")
You are welcome, BioLite!
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