getSignaturesForFitting: getSignaturesForFitting

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

getSignaturesForFitting

Description

Given a tissue type/organ, this function returns the common and rare mutational signatures to be used with FitMS, as suggested in Degasperi et al. 2022, Science paper.

Usage

getSignaturesForFitting(
  organ,
  typemut = "subs",
  commontier = "T1",
  raretier = "T2",
  verbose = TRUE
)

Arguments

organ	organs available are: "Biliary", "Bladder", "Bone_SoftTissue", "Breast", "CNS", "Colorectal", "Esophagus", "Head_neck", "Kidney", "Liver", "Lung", "Lymphoid", "Myeloid", "NET", "Oral_Oropharyngeal", "Ovary", "Pancreas", "Prostate", "Skin", "Stomach", "Uterus"
typemut	only subs and DNV supported at the moment
commontier	is either T1, T2 or T3. The default option is T1. For each organ, T1 indicates to use the common organ-specific signatures, while T2 indicates to use the corresponding reference signatures. In general, T1 should be more appropriate for organs where there are no mixed organ-specific signatures, e.g. GEL-Ovary_common_SBS1+18, while T2 might be more suitable for when such mixed signatures are present, so that each signature can be fitted, e.g. fitting the two signatures SBS1 and SBS18, instead of a single GEL-Ovary_common_SBS1+18. T3 is an intermediate option between T1 and T2, where only the mixed organ signatures are replaced with the corresponding reference signatures.
raretier	is either T0, T1, T2, T3 or T4. The default option is T2. For each organ, T0 are rare signatures that were observed in the requested organ, including low quality signatures (QC amber and red signatures). T1 are high quality (QC green) rare signatures that were observed in the requested organ. T2-T4 signatures extend the rare signatures set to what has been observed also in other organs. T2 includes all QC green signatures found in other organs, with the additional restriction in the case of SBS that the additional signatures were classified as rare at least twice in Degasperi et al. 2022 Science. T3 includes all QC green signatures (if not SBS, T3=T2). T4 includes all signatures including QC amber and red. In general we advise to use the rare T2 tier.

Value

list of signatures matrix

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.