plotVarExplained {BioMM}R Documentation

Plot data summary statistics

Description

Plot data summary statistics in terms of the proportion of variance explained.

Usage

plotVarExplained(data, posF = TRUE, stratify = c("gene", "pathway",
  "chromosome"), core = MulticoreParam(), fileName = NULL)

Arguments

data

The input dataset (either data.frame or matrix). Rows are the samples, columns are the probes/genes, except that the first column is the label (the outcome).

posF

A logical value indicating if only positively outcome-associated features should be used. (Default: TRUE)

stratify

A string. The applied stratification method to generate blocklist. Valid options are c('gene', 'pathway', 'chromosome').

core

The number of cores used for computation. (Default: 1)

fileName

The file name specified for the plot. If it is not NULL, then the plot will be generated. The plot will project the data on the first two components. (Default: 'R2explained.png')

Value

An output image file with '.png' format.

References

Yu, Guangchuang, et al. 'clusterProfiler: an R package for comparing biological themes among gene clusters.' Omics: a journal of integrative biology 16.5 (2012): 284-287.

Perlich, C., & Swirszcz, G. (2011). On cross-validation and stacking: Building seemingly predictive models on random data. ACM SIGKDD Explorations Newsletter, 12(2), 11-15.


[Package BioMM version 1.0.0 Index]