inst/RunScripts/Run_VarSelection_GLM.R

In protViz/SRMService: Report Quantitative Mass Spectrometry Data

library(reshape2)
library(plyr)
library(dplyr)
library(quantable)
library(SRMService)



packagedir <- path.package("SRMService")
longm <-
  read.csv(
    file.path(packagedir, "samples/immunoLongFormat.txt"),
    row.names = 1,
    stringsAsFactors = F
  )

longm$Intensity <- log2(longm$Intensity + 1)
longm$Protein <- longm$Variable


data2Conditions$Condition[data2Conditions$Condition == "Healthy" |
                            data2Conditions$Condition == "Gingivitis"] <- "NonPeriodontitis"
data2Conditions$Condition[(data2Conditions$Condition == "Aggressive" |
                             data2Conditions$Condition == "Chronic")] <- "Periodontitis"

unique(data2Conditions$Condition)

protData <- Protein$new(data2Conditions)


comparisonName <- "Periodontitis vs NonPeriodontitis"
rmarkdown::render(
  "VariableSelection_ROCSingleProtein.Rmd",
  output_format = "html_document",
  output_file = paste("ROC2GroupPeriodontitisVSNon.html", sep =
                        ""),
  clean = FALSE
)
rmarkdown::render(
  "VariableSelection_ROCSingleProtein.Rmd",
  output_format = "pdf_document",
  output_file = paste("ROC2GroupPeriodontitisVSNon.pdf", sep =
                        "") ,
  clean = FALSE
)


tmplong <- longm
nvariables <- 3


Condition2Compare <- "NonPeriodontitis"

rmarkdown::render("VariableSelection_GLM.Rmd",
                  output_file = "SelectVarsNonParandonditisVSParandontitis.html",
                  clean = FALSE)

rmarkdown::render(
  "VariableSelection_GLM.Rmd",
  output_format = "pdf_document",
  output_file = "SelectVarsNonParandonditisVSParandontitis.pdf",
  clean = FALSE
)