pca {ASICS} | R Documentation |
SummarizedExperiment
objectPerform a PCA with the function of the ropls
package on a
SummarizedExperiment
object obtained from the
formatForAnalysis
function
pca( analysis_data, scale.unit = TRUE, type.data = "quantifications", condition = NULL )
analysis_data |
A |
scale.unit |
Logical. If |
type.data |
Type of data used for the analysis (e.g.,
|
condition |
The name of the design variable (two level factor) specifying the groups, if one is available. Default to NULL, no group provided. |
A S4 object of class AnalysisResults containing PCA 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) # Create object for analysis and remove features with more than 25% of # zeros analysis_obj <- formatForAnalysis(quantification, zero.threshold = 25) res_pca <- pca(analysis_obj) }