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andremolan / ADAM_stats_01
Last active October 10, 2018 17:21
Loading ADAM and Aedes gene sample fragment
library(ADAM)
data("ExpressionAedes")
head(ExpressionAedes)
@andremolan
andremolan / ADAM_stats_02
Last active October 10, 2018 17:26
Defining sample comparisons of Aedes aegypti gene expression fragment
Comparison <- c("control1,experiment1","control2,experiment2")
@andremolan
andremolan / ADAM_stats_03
Created October 11, 2018 12:25
Minimum and maximum number of genes per GFAG
Minimum <- 3L
Maximum <- 20L
@andremolan
andremolan / ADAM_stats_04
Last active October 11, 2018 12:33
Seed bootstrap and bootstrap number
SeedBootstrap <- 1049
StepsBootstrap <- 10000L
@andremolan
andremolan / ADAM_stats_05
Created October 11, 2018 12:28
P-value mehtod correction and cuttoff value
CutoffValue <- 0.05
MethodCorrection <- "fdr"
@andremolan
andremolan / ADAM_stats_06
Created October 11, 2018 12:30
Loading KEGG pathways fragment file as an own gene annotation file
data("KeggPathwaysAedes")
head(KeggPathwaysAedes)
@andremolan
andremolan / ADAM_stats_07
Created October 11, 2018 12:32
Domain analysis and gene nomenclature used according to own gene annotation file
Domain <- "own"
Nomenclature <- "gene"
@andremolan
andremolan / ADAM_stats_08
Created October 11, 2018 12:35
Wilcoxon and Fisher test
Wilcoxon <- TRUE
Fisher <- TRUE
@andremolan
andremolan / ADAm_stats_09
Created October 11, 2018 12:39
Running GFAGAnalysis function and returning its value (a list) to a specific variable
ResultAnalysis <- GFAGAnalysis(ComparisonID = Comparison,
ExpressionData = ExpressionAedes,
MinGene = Minimum,
MaxGene = Maximum,
SeedNumber = SeedBootstrap,
BootstrapNumber = StepsBootstrap,
PCorrection = CutoffValue,
DBSpecies = KeggPathwaysAedes,
PCorrectionMethod = MethodCorrection,
WilcoxonTest = Wilcoxon,
@andremolan
andremolan / ADAM_stats_10
Created October 11, 2018 12:52
Accessing and saving results from GFAGAnalysis function
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)