andremolan
andremolan
andremolan
/ ADAM_stats_10
Created Oct 11, 2018
Accessing and saving results from GFAGAnalysis function
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) |
andremolan
/ ADAm_stats_09
Created Oct 11, 2018
Running GFAGAnalysis function and returning its value (a list) to a specific variable
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 |
andremolan
/ ADAM_stats_07
Created Oct 11, 2018
Domain analysis and gene nomenclature used according to own gene annotation file
View ADAM_stats_07
| Domain <- "own" | |
| Nomenclature <- "gene" |
andremolan
/ ADAM_stats_06
Created Oct 11, 2018
Loading KEGG pathways fragment file as an own gene annotation file
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 |
andremolan
/ ADAM_stats_02
Last active Oct 10, 2018
Defining sample comparisons of Aedes aegypti gene expression fragment
View ADAM_stats_02
| Comparison <- c("control1,experiment1","control2,experiment2") |
View ADAM_stats_01
| library(ADAM) | |
| data("ExpressionAedes") | |
| head(ExpressionAedes) |