Perform SIDISH Screening Analysis

Perform SIDISH Screening Analysis

Usage

DoSIDISH(
  matched_bulk,
  sc_data,
  phenotype,
  label_type = NULL,
  phenotype_class = "survival",
  assay = "RNA",
  sidish_param = list(),
  env_params = list(),
  ...
)

Arguments

matched_bulk

Matrix or data frame of preprocessed bulk RNA-seq expression data (genes x samples). Column names must match names/IDs in phenotype.

sc_data

A Seurat object containing scRNA-seq data to be screened.

phenotype

Phenotype data, either: - Patient survival Data frame with row names matching matched_bulk columns, colnames named "time" and "status"

label_type

Character specifying phenotype label type

phenotype_class

Type of phenotypic outcome (must be consistent with input data): - "survival": Survival infomation

assay

Seurat assay name, default: "RNA".

sidish_param

Parameters adjusting SIDISH. Use SigBridgeR:::SIDISHParamSet() to see all available parameters and fetch default values.

env_params

Parameters adjusting python environment. Use SigBridgeR:::SIDISHEnvSet()to see all available parameters and fetch default values.

...

Additional arguments passed to the function. Common parameters include:

verbose

Logical. Whether to print verbose output (default: TRUE).

Value

A named list containing:

scRNA_data

Modified single-cell data object with integrated screening results.

See also

Other screen_method: DoDEGAS(), DoLP_SGL(), DoPIPET(), DoSCIPAC(), DoScissor(), DoscAB(), DoscPAS(), DoscPP()