# TODO: Add comment
#
# Author: erikahrne
###############################################################################
### INIT
if(file.exists("/Users/erikahrne/dev/R/workspace/apmsTools/inst/testData/")){
kBaseDir <- "/Users/erikahrne/dev/R/workspace/apmsTools/inst/"
source("/Users/erikahrne/dev/R/workspace/apmsTools/R/apmsExp.R")
}else{
library(apmsTools)
kBaseDir <- path.package("apmsTools")
}
scaffoldTargetFile <- paste(kBaseDir,"/testData/PP2A-p53.xls",sep="/")
scaffoldControlFile <- paste(kBaseDir,"/testData/GFP5.xls",sep="/")
scaffoldControlNonRedundantFile <- paste(kBaseDir,"/testData/GFP_non-redundant_protein_cluster_analysis.xls",sep="/")
fastaFile <- paste(kBaseDir,"/testData/c_human_TG.decoy_Dehio_Ficproteins_04112013.fasta",sep="")
aExp <- apmsExp(readScaffoldSpecCountFile(scaffoldTargetFile)
,readScaffoldSpecCountFile(scaffoldControlNonRedundantFile, isControl=T))
### INIT END
### TESTS
testReadScaffoldSpecCountFile <-function(){
cat("--- testReadScaffoldSpecCountFile: --- \n")
stopifnot(all.equal(nrow(readScaffoldSpecCountFile(scaffoldTargetFile)),565))
stopifnot(all.equal(nrow(readScaffoldSpecCountFile(scaffoldControlFile)),450))
stopifnot(all.equal(nrow(readScaffoldSpecCountFile(scaffoldControlNonRedundantFile)),655))
cat("--- testReadScaffoldSpecCountFile: PASS ALL TEST --- \n")
}
testApmsExp <-function(){
cat("--- testApmsExp: --- \n")
stopifnot(all.equal(ncol(apmsExp(readScaffoldSpecCountFile(scaffoldTargetFile)
,readScaffoldSpecCountFile(scaffoldControlNonRedundantFile))$specCountDf)
,11))
cat("--- testApmsExp: PASS ALL TEST --- \n")
}
testWriteSaintBaitFile <- function(){
cat("--- testWriteSaintBaitFile --- ")
writeSaintBaitFile(aExp,paste(tempdir(),"bait.txt",sep="/"),verbose=T)
cat("--- testWriteSaintBaitFile: PASS ALL TEST --- \n")
}
testWriteSaintInteractionFile <- function(){
cat("--- testWriteSaintInteractionFile: --- ")
writeSaintInteractionFile(aExp,paste(tempdir(),"interaction.txt",sep="/"),verbose=T)
cat("--- testWriteSaintInteractionFile: PASS ALL TEST --- \n")
}
testWriteSaintPreyFile <- function(){
cat("--- writeSaintPreyFile: --- ")
writeSaintPreyFile(aExp,paste(tempdir(),"prey.txt",sep="/"),verbose=T)
cat("--- testWriteSaintPreyFile: PASS ALL TEST --- \n")
}
testSetProteinLength <- function(){
cat("--- testSetProteinLength: ---" ,stopifnot(all.equal(setProteinLength(aExp,fastaFile)$specCountDf$proteinLength[565],222)),"\n")
cat("--- testSetProteinLength: PASS ALL TEST --- \n")
}
testWriteCRAPomeFile <-function(){
cat("--- testWriteCRAPomeFile: --- ")
writeCRAPomeFile(aExp,paste(tempdir(),"CRAPome_input.tsv",sep="/"),verbose=T)
cat("--- testWriteCRAPomeFile: PASS ALL TEST --- \n")
}
### TESTS END
### RUN TESTS
testReadScaffoldSpecCountFile()
testApmsExp()
testWriteSaintBaitFile()
testWriteSaintInteractionFile()
testWriteSaintPreyFile()
testSetProteinLength()
testWriteCRAPomeFile()
### RUN TESTS END
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