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View gist:6fe0124fef2a6c389325ee65ecd32900
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#Packages from CRAN repository
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install.packages(c("Rcpp","pbapply","dplyr","BiocManager"))
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#Packages from Bioconductor
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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",
View 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)
View 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,
View ADAM_stats_08
Wilcoxon <- TRUE
Fisher <- TRUE
View ADAM_stats_07
Domain <- "own"
Nomenclature <- "gene"
View ADAM_stats_06
data("KeggPathwaysAedes")
head(KeggPathwaysAedes)
View ADAM_stats_05
CutoffValue <- 0.05
MethodCorrection <- "fdr"
View ADAM_stats_04
SeedBootstrap <- 1049
StepsBootstrap <- 10000L
View ADAM_stats_03
Minimum <- 3L
Maximum <- 20L
View ADAM_stats_02
Comparison <- c("control1,experiment1","control2,experiment2")