trendSceek#

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Last Updated: Mar 11, 2023

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: doi:10.1038/nmeth.4634

Value#

data.frame with trendsceek spatial genes results