kruskalWallis {ASICS} | R Documentation |
SummarizedExperiment
objectPerform Kruskal-Wallis tests on a SummarizedExperiment
object
obtained with the formatForAnalysis
function
kruskalWallis( analysis_data, condition, alpha = 0.05, type.data = "quantifications", ... )
analysis_data |
A |
condition |
The name of the design variable (two level factor) specifying the group of each sample. |
alpha |
Cutoff for adjusted p-values. Default to 0.05. |
type.data |
Type of data used for the analyses (e.g., |
... |
Arguments to be passed to |
A S4 object of class AnalysisResults containing test results.
# Import quantification results if (require("ASICSdata", quietly = TRUE)) { quantif_path <- system.file("extdata", "results_ASICS.txt", package = "ASICSdata") quantification <- read.table(quantif_path, header = TRUE, row.names = 1) # Import design design <- read.table(system.file("extdata", "design_diabete_example.txt", package = "ASICSdata"), header = TRUE) design$condition <- factor(design$condition) # Create object for analysis and remove features with more than 25% of # zeros analysis_obj <- formatForAnalysis(quantification, zero.threshold = 25, design = design) res_tests <- kruskalWallis(analysis_obj, "condition", method = "BH") }