PVCA: Performs a Principal Variance Component Analysis (PVCA) and...

In sistm/sistmr: A Collection of Utility Functions from the Inserm/Inria SISTM Team

Performs a Principal Variance Component Analysis (PVCA) and output the plot

Description

Performs a Principal Variance Component Analysis (PVCA) and output the plot

Usage

PVCA(
  expression,
  sample_info,
  Sample_ID,
  effects,
  pct_threshold = 0.95,
  verbose = FALSE,
  title = "PVCA",
  ...
)

Arguments

expression	numeric matrix of gene expressions with sample IDs as colnames and gene/probes in rows
sample_info	a data.frame containing the design and technical informations on the samples.
Sample_ID	the name of the column in sample_info which contain the sample IDs and which should match colnames(expression) in the same order.
effects	the name of the columns from sample_info which should be investigated for potential Batch effect
pct_threshold	a value between 0 and 1 (Default is 0.95). The percentile value of the minimum amount of the variabilities that the selected principal components need to explain.
verbose	a logical indicating if information about method's progress must be printed. Default is FALSE.
title	the title of the barplot.
...	others parameters to be passed into the barplot.

Value

a barplot.

Author(s)

Boris Hejblum

References

Adapted from Pierre R. Bushel original programm (email: [e-mail])

sistm/sistmr documentation built on March 8, 2024, 3:05 a.m.