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.
<- system.file("extdata", "cosmic2_record_by_cancer.rds", package = "sigminer")
db1 <- readRDS(db1)
db1 colnames(db1) <- c("Cancer type", "Signature Index")
<- system.file("extdata", "signature_record_by_cancer.rds", package = "sigminer")
db2 <- readRDS(db2)
db2 colnames(db2) <- c(
"Cancer type", "Cohort", "Sequencing strategy",
"SBS signature index",
"DBS signature index",
"ID signature index"
)
::datatable(db1, caption = "Data source: https://cancer.sanger.ac.uk/signatures_v2/matrix.png") DT
Note, set
sig_db
to ‘legacy’ (the default) insig_fit()
family functions.
::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") DT