starfish_sig: starfish_sig

In yanglab-computationalgenomics/Starfish: Detecting connected CGR regions and inferring mechanisms from structural variation and copy number data

starfish_sig

Description

This function loads the CGR feature matrix and perform clustering and classification.

Usage

starfish_sig(
  cluster_feature,
  prefix = "",
  cmethod = "class",
  pcawg_feature = pcawg_chrss_raw,
  class_model = nn_model
)

Arguments

cluster_feature	the CGR feature matrix, output from starfish_feature
prefix	prefix for intermediate files, default is none
cmethod	"class" based on a pre-constructed classifier or "cluster" based on de-novo unsupervised clustering, default is "class"

Value

The signature classification table and plot if "class" is selected.The clustering results are stored under "CGR_cluster" folder if "cluster" is selected. $cluster_id contains CGR event IDs, and $CGR_signature shows the signature names used in the PCAWG paper.

yanglab-computationalgenomics/Starfish documentation built on July 27, 2022, 10:26 a.m.