plotCoefficients: Plot coefficients for a gene expression meta-analysis.

In jakejh/metapredict: Meta-analysis of gene expression using the elastic net

Plot coefficients for a gene expression meta-analysis.

Description

Make a ggplot of the coefficients from a glmnet object trained on a gene expression meta-analysis (either logistic or multinomial classification).

Usage

plotCoefficients(
  fitResult,
  lambda,
  classLevels = NA,
  decreasing = FALSE,
  geneIdOrder = NA,
  org = "org.Hs.eg"
)

Arguments

fitResult	glmnet object.
lambda	value of lambda to use in fitResult.
classLevels	Order of classes in the confusion matrix. If NA (default), then the function uses the order in fitResult.
decreasing	logical indicating whether to sort genes by decreasing coefficient.
geneIdOrder	Optional character array of Entrez Gene IDs specifying the order of genes. If NA (default), the order from makeCoefDt() is used.
org	Name of package for mapping Entrez Gene IDs to gene symbols, passed to data argument of annotate::lookUp().

Value

A ggplot object.

jakejh/metapredict documentation built on Feb. 14, 2023, 7:53 p.m.