selectPatternGenes: selectPatternGenes

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Select genes correlated with spatial patterns

Usage

selectPatternGenes(
  spatPatObj,
  dimensions = 1:5,
  top_pos_genes = 10,
  top_neg_genes = 10,
  min_pos_cor = 0.5,
  min_neg_cor = -0.5,
  return_top_selection = FALSE
)

Arguments

spatPatObj	Output from detectSpatialPatterns
dimensions	dimensions to identify correlated genes for.
top_pos_genes	Top positively correlated genes.
top_neg_genes	Top negatively correlated genes.
min_pos_cor	Minimum positive correlation score to include a gene.
min_neg_cor	Minimum negative correlation score to include a gene.
return_top_selection	only return selection based on correlation criteria (boolean)

Details

Description.

Value

Data.table with genes associated with selected dimension (PC).

Examples

    selectPatternGenes(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.