README.md

In CBIIT/rcellminerElasticNet: rcellminerElasticNet

install RCellMiner in R 3.2.*

source("https://bioconductor.org/biocLite.R") biocLite("rcellminer") biocLite("rcellminerData")

Open Project

Open Rproj file in RStudio

Install Dependencies

if (!"devtools" %in% installed.packages()) install.packages("devtools")

setRepositories(ind=1:6)
library(devtools)

install_bitbucket("cbio_mskcc/rcellminerelasticnet",
  auth_user="discoverUser",
  password="discoverUserPassword",
  build_vignettes=FALSE,
  dependencies=TRUE,
  args="--no-multiarch")

# Custom pheatmap version  
install_github("cannin/pheatmap", dependencies=TRUE)

Run Vignette

Open vignette (Rmd files) from vignettes/ folder and use "Knit HTML" button to generate the HTML file.

Download RData files

wget -r -nH -N -R index.html http://cmuser:[e-mail]/swathAnalysis/

Convert Rmd to R

library(knitr); purl(file.path("vignettes", "checkEnData.Rmd"), output=file.path("vignettes", "checkEnData.R")) library(knitr); purl(file.path("vignettes", "makeEnResultsHeatmap.Rmd"), output=file.path("vignettes", "makeEnResultsHeatmap.R")) library(knitr); purl(file.path("vignettes", "makeEnResultsTable.Rmd"), output=file.path("vignettes", "makeEnResultsTable.R"))

Command to obtain elastic net errors

grep -h "## Error" *.html | sort -u

Errors due to empty elastic net feature set

## Error in .Method(..., na.last = na.last, decreasing = decreasing): argument 1 is not a vector
## Error in apply(cvFoldEnPredictorWts, MARGIN = 1, FUN = function(x) {: dim(X) must have a positive length
## Error in kable_markdown(x = structure(character(0), .Dim = c(0L, 0L), .Dimnames = list(: the table must have a header (column names)
## Error in sqrt(elNetResults$fullEnCvResults$cvPredRsqared): non-numeric argument to mathematical function
## Error: identical(names(reducedFeatureSetAvgWts), names(reducedFeatureSetNonzeroWtPct)) is not TRUE

Errors from missing data
## Error in molDB[[molDBType]][paste0(molDBType, includeFeatures), ]: subscript out of bounds

CBIIT/rcellminerElasticNet documentation built on Sept. 8, 2020, 6:21 p.m.