PCASigGenes: Significant genes from a PCA

In Seurat: Tools for Single Cell Genomics

Significant genes from a PCA

Description

Returns a set of genes, based on the JackStraw analysis, that have statistically significant associations with a set of PCs.

Usage

PCASigGenes(
  object,
  pcs.use,
  pval.cut = 0.1,
  use.full = FALSE,
  max.per.pc = NULL
)

Arguments

object	Seurat object
pcs.use	PCS to use.
pval.cut	P-value cutoff
use.full	Use the full list of genes (from the projected PCA). Assumes that ProjectDim has been run. Currently, must be set to FALSE.
max.per.pc	Maximum number of genes to return per PC. Used to avoid genes from one PC dominating the entire analysis.

Value

A vector of genes whose p-values are statistically significant for at least one of the given PCs.

See Also

ProjectDim JackStraw

Examples

data("pbmc_small")
PCASigGenes(pbmc_small, pcs.use = 1:2)

Seurat documentation built on May 29, 2024, 4:20 a.m.