andremolan

###
#Pacotes do repositório CRAN
###
install.packages(c("Rcpp","pbapply","dplyr","BiocManager","DT","stringr","knitr"))

###
#Pacotes do repositório Bioconductor
###
BiocManager::install("GO.db","KEGGREST","SummarizedExperiment")

andremolan

###
#Packages from CRAN repository
###
install.packages(c("Rcpp","pbapply","dplyr","BiocManager","DT","stringr","knitr"))

###
#Packages from Bioconductor
###
BiocManager::install("GO.db","KEGGREST","SummarizedExperiment")                     

andremolan

GenesGFAGs <- ResultAnalysis[[1]]
Comparison_1 <- ResultAnalysis[[2]][1]
Comparison_2 <- ResultAnalysis[[2]][2]

write.table(GenesGFAGs, file = "GenesGFAGs.txt", quote = FALSE, sep = "\t",
            row.names = FALSE, col.names = TRUE)

write.table(Comparison_1, file = "Comparison_1.txt", quote = FALSE, sep = "\t",
            row.names = FALSE, col.names = TRUE)

andremolan

ResultAnalysis <- GFAGAnalysis(ComparisonID = Comparison, 
                               ExpressionData = ExpressionAedes,
                               MinGene = Minimum,
                               MaxGene = Maximum,
                               SeedNumber = SeedBootstrap, 
                               BootstrapNumber = StepsBootstrap,
                               PCorrection = CutoffValue,
                               DBSpecies = KeggPathwaysAedes, 
                               PCorrectionMethod = MethodCorrection,
                               WilcoxonTest = Wilcoxon,

andremolan

Wilcoxon <- TRUE
Fisher <- TRUE

andremolan

Domain <- "own"
Nomenclature <- "gene"

andremolan

data("KeggPathwaysAedes")
head(KeggPathwaysAedes)

andremolan

CutoffValue <- 0.05
MethodCorrection <- "fdr"

andremolan

SeedBootstrap <- 1049
StepsBootstrap <- 10000L

andremolan

Minimum <- 3L
Maximum <- 20L