tl_RunPCAScore: a robust PCA for Seurat

In zzwch/convgene: This package is designed to conveniently convert gene between human and mouse.

Description

Based on a pre-computed dimensional reduction (typically calculated on a subset of genes and projects this onto the entire dataset (all genes). Then generate a new rPCA reduction.

Usage

tl_RunPCAScore(
  object,
  slot = "data",
  assay = NULL,
  reduction = "pca",
  use_all_genes = T,
  topn = 30,
  do.score.scale = T,
  reduction.name = "rpca"
)

Arguments

object	Seurat3 object
slot	use which data to calc rpca
assay	use which assay. NULL to use DefaultAssay(object)
reduction	use which reduction to obtain top features.
use_all_genes	get top n genes from all genes loadings, not just typically highly variable genes. This will call ProjectDim if inexist.
topn	robust top n genes of loadings
do.score.scale	scale robust scores
reduction.name	new reduction name

Value

updated Seurat3 object with a new pca_score reduction added

zzwch/convgene documentation built on July 11, 2021, 9:41 a.m.