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View ADAM_stats_01_PB
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#Pacotes do repositório CRAN
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install.packages(c("Rcpp","pbapply","dplyr","BiocManager","DT","stringr","knitr"))
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#Pacotes do repositório Bioconductor
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BiocManager::install("GO.db","KEGGREST","SummarizedExperiment")
View ADAM_stats_01_EN
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#Packages from CRAN repository
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install.packages(c("Rcpp","pbapply","dplyr","BiocManager","DT","stringr","knitr"))
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#Packages from Bioconductor
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BiocManager::install("GO.db","KEGGREST","SummarizedExperiment")
@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
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,
@andremolan
andremolan / ADAM_stats_08
Created Oct 11, 2018
Wilcoxon and Fisher test
View ADAM_stats_08
Wilcoxon <- TRUE
Fisher <- TRUE
@andremolan
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
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)
@andremolan
andremolan / ADAM_stats_05
Created Oct 11, 2018
P-value mehtod correction and cuttoff value
View ADAM_stats_05
CutoffValue <- 0.05
MethodCorrection <- "fdr"
@andremolan
andremolan / ADAM_stats_04
Last active Oct 11, 2018
Seed bootstrap and bootstrap number
View ADAM_stats_04
SeedBootstrap <- 1049
StepsBootstrap <- 10000L
@andremolan
andremolan / ADAM_stats_03
Created Oct 11, 2018
Minimum and maximum number of genes per GFAG
View ADAM_stats_03
Minimum <- 3L
Maximum <- 20L
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