pca_plot: Generate principal component analysis plots from normalized...

In kevinlul/EpigeneLite: Lite version of EpigenCentral

Description

Generate principal component analysis plots from normalized methylation beta values. By default, this will do this for all CpGs, however, you can pass in a data frame of specific ones of interest to only consider differentially methylated CpGs.

Usage

pca_plot(grset, df_dmps = NULL)

Arguments

grset	minfi GenomicRatioSet containing beta values
df_dmps	optional data frame of CpGs of interest

Value

ggplot2 PCA plot

References

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

Examples

## Not run: 
grset <- read_geo_tsv("extdata/GSE55491/GSE55491_series_matrix.txt")
pca_plot(grset)

## End(Not run)

kevinlul/EpigeneLite documentation built on Dec. 21, 2021, 6:35 a.m.