andremolan’s gists

## gist:6fe0124fef2a6c389325ee65ecd32900
###
#Packages from CRAN repository
###
install.packages(c("Rcpp","pbapply","dplyr","BiocManager"))

###
#Packages from Bioconductor
###
BiocManager::install("GO.db","KEGGREST","DT","SummarizedExperiment","org.Ag.eg.db","org.At.tair.db","org.Bt.eg.db",
                     "org.Ce.eg.db","org.Cf.eg.db","org.Dm.eg.db","org.Dr.eg.db","org.EcK12.eg.db","org.EcSakai.eg.db",

## ADAM_stats_10
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)

## ADAm_stats_09
ResultAnalysis <- GFAGAnalysis(ComparisonID = Comparison,
                               ExpressionData = ExpressionAedes,
                               MinGene = Minimum,
                               MaxGene = Maximum,
                               SeedNumber = SeedBootstrap,
                               BootstrapNumber = StepsBootstrap,
                               PCorrection = CutoffValue,
                               DBSpecies = KeggPathwaysAedes,
                               PCorrectionMethod = MethodCorrection,
                               WilcoxonTest = Wilcoxon,

## ADAM_stats_08
Wilcoxon <- TRUE
Fisher <- TRUE

## ADAM_stats_07
Domain <- "own"
Nomenclature <- "gene"

## ADAM_stats_06
data("KeggPathwaysAedes")
head(KeggPathwaysAedes)

## ADAM_stats_05
CutoffValue <- 0.05
MethodCorrection <- "fdr"

## ADAM_stats_04
SeedBootstrap <- 1049
StepsBootstrap <- 10000L

## ADAM_stats_03
Minimum <- 3L
Maximum <- 20L

## ADAM_stats_02
Comparison <- c("control1,experiment1","control2,experiment2")