Seurat: PCASigGenes – R documentation

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PCASigGenes

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.

Examples

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

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17