pca_highscores: Get the highest/lowest scoring genes for every principle...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Get the highest/lowest scoring genes for every principle component.

Description

This function uses princomp to acquire a principle component biplot for some data and extracts a dataframe of the top n genes for each component by score.

Usage

pca_highscores(expt, n = 20, cor = TRUE, vs = "means", logged = TRUE)

Arguments

expt	Experiment to poke.
n	Number of genes to extract.
cor	Perform correlations?
vs	Do a mean or median when getting ready to perform the pca?
logged	Check for the log state of the data and adjust as deemed necessary?

Value

a list including the princomp biplot, histogram, and tables of top/bottom n scored genes with their scores by component.

See Also

[stats] [stats::princomp]

Examples

## Not run: 
 information <- pca_highscores(df = df, conditions = cond, batches = bat)
 information$pca_bitplot  ## oo pretty

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.