process_input_seurat: Extract differentially expressed genes from Seurat object
In AhmedMehdiLab/E.PAGE: Environmental Pathways Affecting Gene Expression

process_input_seurat

R Documentation

Extract differentially expressed genes from Seurat object

Finds differentially expressed genes, records adjusted P-value and filters for values less than max_p.

process_input_seurat(
  seurat,
  id_1,
  id_2 = NULL,
  group = NULL,
  cluster = NULL,
  max_p = 0.05
)

`seurat`	Seurat object
`id_1`	first identity
`id_2`	optional: second identity; default all others
`group`	optional: subgroup of cluster
`cluster`	optional: cluster selected
`max_p`	P-value cutoff, only genes with P-values less than this will be returned

tibble: "gene" gene names "value" gene values

seu_path <- system.file("extdata", "ex_seurat.rds", package = "E.PAGE")
seurat <- readRDS(seu_path)

input <- process_input_seurat(seurat, 0)

AhmedMehdiLab/E.PAGE documentation built on Aug. 21, 2022, 4:37 p.m.

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