Parameter choices

Tumor type and data tags

Using list_tumor_types() function you can see the options for tumor_type parameter for the run() function, similarly use list_data_options() to see the available data parameters. You can see if the SNV counts in your data aggrees with the mutation counts in the datasets for tuning the gradient boosting classifiers by running info(data, tumor_type). If the values disagree the cutoffs on the score listed in Signature_3_mva column of SigMA output needs to be optimized or a new model needs to be tuned.

Tags and descriptions of performance of SigMA for signature 3 detection. The exploratory tumor types should be used with do_mva = F and do_assign = F settings for the run() function for these tumor types if you want to investigate presence of Signature_3 set add_sig3 = T which will then allow assignment of Signature 3 to the tumors even if this signature was not discovered by NMF in the WGS data for these tumor types.

Tumor types with tuned MVA models

Tumor type	Tag	Platform
Urothelial Bladder Cancer	bladder	Panel/Exome/WGS
Breast Cancer	breast	Panel/Exome/WGS
Oesophageal Carcinoma	eso	Panel/Exome/WGS
Ewing Sarcoma	ewing	Exome/WGS
Leiomyosarcoma	lms	Panel/Exome/WGS
Medulloblastoma	medullo	Exome/WGS
Osteosarcoma	osteo	Panel/Exome/WGS
Ovarian Cancer	ovary	Panel/Exome/WGS
Pancreas Adenocarcinoma	panc_ad	Panel/Exome/WGS
Pancreas Neuroendocrine	panc_en	Panel/Exome/WGS
Prostate Adenocarcinoma	prost	Panel/Exome/WGS
Stomach Adenocarcinoma	stomach	Panel/Exome/WGS
Uterine corpus endometrial carcinoma	uterus	Panel/Exome/WGS

Tumor types without tuned MVA models but with references calculated based on WGS

Tumor type	Tag
Biliary Tract Cancer	biliary
Cervical Cancer	cervix
Colorectal Adenocarcinoma	crc
Glioblastoma	glioma
Head and Neck Cancer	head
Leukemia	leuk
Lung Adenocarcinoma	lung
Lymphoma	lymph
Thyroid Cancer	thyroid