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Run scMalignantFinder malignant spatial region identification

Source: R/RunscMalignantFinder.R
RunscMalignantRegion.Rd

Use scMalignantFinder spatial utilities to score malignant signatures and infer malignant spatial regions. For Seurat input, provide spatial.cols when spatial-neighborhood refinement is requested and the converted AnnData object does not already contain spatial coordinates.

Usage

RunscMalignantRegion(
  srt = NULL,
  adata = NULL,
  h5ad = NULL,
  assay = "RNA",
  layer = "counts",
  cells = NULL,
  signature_gmt,
  features = NULL,
  nclus = 3,
  define_feature = "Malignant_up",
  spatial_nn = TRUE,
  spatial.cols = NULL,
  spatial_key = "spatial",
  image = FALSE,
  norm_type = NULL,
  prefix = "scMalignantFinder_",
  return_seurat = !is.null(srt),
  verbose = TRUE
)

Arguments

srt

A Seurat object.

adata

Optional Python AnnData object.

h5ad

Optional path to an .h5ad file.

assay

Assay used when srt is supplied. Default is "RNA".

layer

Layer used when srt is supplied. Default is "counts".

cells

Optional cells to run. If supplied with srt, results are appended to these cells and other cells receive NA.

signature_gmt

Path to the malignant signature .gmt file, such as sc_malignant_deg.gmt from the scMalignantFinder resources.

features

Features in adata.obs used for region clustering. If NULL, uses malignancy_probability and Malignant_up, plus image_score when image = TRUE.

nclus

Number of clusters used by the spatial region model.

define_feature

Feature used to select the malignant region cluster.

spatial_nn

Whether to refine labels by spatial neighbors.

spatial.cols

Optional two metadata columns used as spatial coordinates for Seurat input.

spatial_key

Key written to adata.obsm for spatial coordinates.

image

Whether to call scMalignantFinder.spatial.image_cal. Default is FALSE because Seurat-to-AnnData conversion does not generally carry histology images.

norm_type

Passed to scMalignantFinder. Use TRUE for raw counts that should be library-size normalized; use FALSE for already normalized input. If NULL, defaults to TRUE only for Seurat counts input.

prefix

Optional prefix for output metadata columns. Default preserves the original scMalignantFinder column names.

return_seurat

Whether to return a Seurat object when srt is supplied. If FALSE, returns a data frame of predictions.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with malignant region metadata, or a data frame when return_seurat = FALSE.

Examples

if (FALSE) {
srt <- RunscMalignantRegion(
  srt,
  signature_gmt = "path/to/sc_malignant_deg.gmt",
  spatial.cols = c("x", "y")
)
}