compare_pc_sv: Incomplete function to compare PCs and SVs.

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

Incomplete function to compare PCs and SVs.

Description

This function is the beginning of a method to get a sense of what happens to data when performing things like SVA.

Usage

compare_pc_sv(
  expt,
  norm = NULL,
  transform = "log2",
  convert = "cpm",
  filter = TRUE,
  batch = "svaseq"
)

Arguments

expt	Input expressionset.
norm	Normalization performed.
transform	Assuming using PCA and so log2 the data.
convert	Scale the data, presumably with cpm().
filter	Low-count filter the data?
batch	Method which provides SVs to apply.

Value

Currently just a plot of the SVs.

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