restrict_counts: Restricts a SpatialRNA object to a subset of genes (and...

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Restricts a SpatialRNA object to a subset of genes (and applies a UMI threshold)

Description

Restricts a SpatialRNA object to a subset of genes (and applies a UMI threshold)

Usage

restrict_counts(
  puck,
  gene_list,
  UMI_thresh = 1,
  UMI_max = 20000,
  counts_thresh = 1
)

Arguments

puck	a SpatialRNA object
gene_list	a list of gene names
UMI_thresh	minimum UMI per pixel
UMI_max	maximum UMI per pixel
counts_thresh	minimum counts per pixel (for genes in gene_list)

Value

Returns a SpatialRNA with counts filtered based on UMI threshold and gene list

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.