explorePCVariability: Compute and plot the results of a PCA analysis on gene...

In bhuvad/restools: Research tools for data science projects

Compute and plot the results of a PCA analysis on gene expression data

Description

Compute and plot the results of a PCA analysis on gene expression data

Usage

explorePCVariability(edata, annots, ...)

## S4 method for signature 'DGEList'
explorePCVariability(edata, annots, maxdim = 25, precomputed = NULL, ...)

## S4 method for signature 'ExpressionSet'
explorePCVariability(edata, annots, maxdim = 25, precomputed = NULL, ...)

## S4 method for signature 'SummarizedExperiment'
explorePCVariability(
  edata,
  annots,
  assay = 1,
  maxdim = 25,
  precomputed = NULL,
  ...
)

Arguments

edata	a DGEList, SummarizedExperiment or ExpressionSet object containing gene expression data.
annots	variables to assess for contributions in each PC. ANOVA is used for categorical variables and linear models for continuous variables.
...	aesthetic mappings to pass to 'ggplot2::aes_string()'.
maxdim	a numeric, specifying the maximum number of dimensions to plot.
precomputed	a dimensional reduction results from 'stats::prcomp'.
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment).

Value

a 'Heatmap-class' object.

Examples

se = emtdata::cursons2015_se()
dge = emtdata::asDGEList(se)
explorePCVariability(dge, c(Subline, Treatment, lib.size))

bhuvad/restools documentation built on June 16, 2024, 12:44 a.m.