perform.sct: Performs SCTransform

In connorhknight/IBRAP_no_decontX: Integrated Benchmarking scRNA-seq Analytical Pipeline

Description

Performs SCTransform normalisation, hvg selection, scaling and variance stabilisation and regression.

Usage

perform.sct(object, assay, slot, new.assay.suffix = "", ...)

Arguments

object	IBRAP S4 class object
assay	A character string containing indicating which assay to use
slot	String indicating which slot within the assay should be sourced
new.assay.suffix	Character. What should be added as a suffix for SCT
do.scale	Whether to scale residuals to have unit variance; default is FALSE
do.center	Whether to center residuals to have mean zero; default is TRUE
vars.to.regress	Character. Which data from 'object@sample_metadata' should be regressed from the dataset.
n.genes	Numerical value of how many highly variable genes should be retained. Default = 1500
min_cells	Numerical value of minimum cells required for a gene to not be filtered. Default = 3

Value

Produces a new 'methods' assay containing normalised, scaled and HVGs.

Examples

object <- perform.sct(object = object, 
                      assay = 'RAW', 
                      slot = 'counts')

connorhknight/IBRAP_no_decontX documentation built on Feb. 13, 2022, 2:32 p.m.