Significant genes from a PCA

Source: R/dimensional_reduction.R

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

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)
#>  [1] "PPBP"     "VDAC3"    "CD1C"     "AKR1C3"   "PF4"      "MYL9"    
#>  [7] "GNLY"     "TREML1"   "CA2"      "SDPR"     "PGRMC1"   "S100A8"  
#> [13] "TUBB1"    "HLA-DQA1" "PARVB"    "RUFY1"    "HLA-DPB1" "S100A9"