Download_DNAmethylation: The Download_DNAmethylation function

Description Usage Arguments Value Examples

View source: R/Download_Preprocess.R

Description

Downloads DNA methylation data from TCGA.

Usage

1
Download_DNAmethylation(CancerSite, TargetDirectory, downloadData = TRUE)

Arguments

CancerSite

character of length 1 with TCGA cancer code.

TargetDirectory

character with directory where a folder for downloaded files will be created.

downloadData

logical indicating if data should be downloaded (default: TRUE). If false, the url of the desired data is returned.

Value

list with paths to downloaded files for both 27k and 450k methylation data.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
## Not run: 

# Optional register cluster to run in parallel
library(doParallel)
cl <- makeCluster(5)
registerDoParallel(cl)

# Methylation data for ovarian cancer
cancerSite <- "OV"
targetDirectory <- paste0(getwd(), "/")

# Downloading methylation data
METdirectories <- Download_DNAmethylation(cancerSite, targetDirectory, TRUE)

# Processing methylation data
METProcessedData <- Preprocess_DNAmethylation(cancerSite, METdirectories)

# Saving methylation processed data
saveRDS(METProcessedData, file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds"))

# Clustering methylation data
res <- ClusterProbes(METProcessedData[[1]], METProcessedData[[2]])

# Saving methylation clustered data
toSave <- list(METcancer = res[[1]], METnormal = res[[2]], ProbeMapping = res$ProbeMapping)
saveRDS(toSave, file = paste0(targetDirectory, "MET_", cancerSite, "_Clustered.rds"))

stopCluster(cl)

## End(Not run)
 

gevaertlab/methylmix documentation built on May 25, 2019, 5:25 p.m.