pca: Principal Component Analysis (PCA) on a...

Description Usage Arguments Value See Also Examples

View source: R/analysis_on_quantification.R

Description

Perform a PCA with the function of the ropls package on a SummarizedExperiment object obtained from the formatForAnalysis function

Usage

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pca(
  analysis_data,
  scale.unit = TRUE,
  type.data = "quantifications",
  condition = NULL
)

Arguments

analysis_data

A SummarizedExperiment object obtained from the formatForAnalysis function.

scale.unit

Logical. If TRUE, data are scaled to unit variance prior PCA.

type.data

Type of data used for the analysis (e.g., "quantifications", "buckets"...). Default to "quantifications".

condition

The name of the design variable (two level factor) specifying the groups, if one is available. Default to NULL, no group provided.

Value

A S4 object of class AnalysisResults containing PCA results.

See Also

AnalysisResults

Examples

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# 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)
}

ASICS documentation built on Nov. 8, 2020, 8:19 p.m.