getMarkerGenes: Get marker genes for every sample and cluster in Seurat...

In romanhaa/cerebroPrepare: Export data for visualization in Cerebro.

Description

This function gets marker genes for every sample and cluster of the Seurat object.

Usage

getMarkerGenes(object, organism = NULL, column_sample = "sample",
  column_cluster = "cluster", only_pos = TRUE, min_pct = 0.7,
  thresh_logFC = 0.25, thresh_p_val = 0.01, test = "wilcox",
  verbose = TRUE, ...)

Arguments

object	Seurat object.
organism	Organism information for pulling info about presence of marker genes of cell surface; can be omitted if already saved in Seurat object; defaults to NULL.
column_sample	Column in [e-mail] that contains information about sample; defaults to 'sample'.
column_cluster	Column in [e-mail] that contains information about cluster; defaults to 'cluster'.
only_pos	Identify only over-expressed genes; defaults to TRUE.
min_pct	Only keep genes that are expressed in at least n% of current group of cells, defaults to 0.70 (70%).
thresh_logFC	Only keep genes that show an average logFC of at least n; defaults to 0.25.
thresh_p_val	Threshold for p-value, defaults to 0.01.
test	Statistical test used, defaults to 'wilcox' (Wilcoxon test).
verbose	Print progress bar; defaults to TRUE.
...	Further parameters can be passed to control Seurat::FindAllMakers().

Details

Get marker genes for every sample and cluster in Seurat object.

Examples

seurat <- getMarkerGenes(
  object = seurat
  organism = 'hg',
  column_sample = 'sample',
  column_cluster = 'cluster',
  only_pos = TRUE,
  min_pct = 0.7,
  thresh_logFC = 0.25,
  thresh_p_val = 0.01,
  test = 'wilcox',
  verbose = TRUE
)

romanhaa/cerebroPrepare documentation built on Oct. 17, 2019, 4:01 p.m.