trendSceek#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L2152

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#

Argument

Description

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

list()

Additional parameters to the `tr endsceek_test <#trendsceektest>`__ function

Details#

This function is a wrapper for the trendsceek_test method implemented in the trendsceek package Publication: c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1038/nmeth.4634?) list(“tools:::Rd_expr_doi(“10.1038/nmeth.4634”)?)

Value#

data.frame with trendsceek spatial genes results