trendSceek: trendSceek

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

trendSceek

Description

Compute spatial variable genes with trendsceek method

Usage

trendSceek(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  spat_loc_name = "raw",
  expression_values = c("normalized", "raw"),
  subset_genes = NULL,
  nrand = 100,
  ncores = 8,
  ...
)

Arguments

gobject	Giotto object
feat_type	feature type
spat_unit	spatial unit
spat_loc_name	name for spatial locations
expression_values	gene expression values to use
subset_genes	subset of genes to run trendsceek on
nrand	An integer specifying the number of random resamplings of the mark distribution as to create the null-distribution.
ncores	An integer specifying the number of cores to be used by BiocParallel
...	Additional parameters to the trendsceek_test function

Details

This function is a wrapper for the trendsceek_test method implemented in the trendsceek package Publication: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nmeth.4634")}

Value

data.frame with trendsceek spatial genes results

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.