Chapter 6 Sigflow Pipeline

Sigflow provides useful mutational signature analysis workflows based on R package sigminer. It can auto-extract mutational signatures, fit mutation data to COSMIC reference signatures (SBS/DBS/INDEL) and run bootstrapping analysis for signature fitting.

For full documentation, please read Sigflow README.

6.1 Cancer type specific signature index database

Signature fitting analysis may befit from directly specifying known signatures identified in a cancer type. We collect such information and provide the following data tables.

db1 <- system.file("extdata", "cosmic2_record_by_cancer.rds", package = "sigminer")
db1 <- readRDS(db1)
colnames(db1) <- c("Cancer type", "Signature Index")
db2 <- system.file("extdata", "signature_record_by_cancer.rds", package = "sigminer")
db2 <- readRDS(db2)
colnames(db2) <- c(
  "Cancer type", "Cohort", "Sequencing strategy",
  "SBS signature index",
  "DBS signature index",
  "ID signature index"
)

DT::datatable(db1, caption = "Data source: https://cancer.sanger.ac.uk/signatures_v2/matrix.png")

Note, set sig_db to ‘legacy’ (the default) in sig_fit() family functions.

DT::datatable(db2[, c(1:3, 4)], caption = "Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3")

DT::datatable(db2[, c(1:3, 5)], caption = "Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3")

DT::datatable(db2[, c(1:3, 6)], caption = "Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3")