simplify_signature: Function to simplify signature representation into...

In TomasettiLab/supersigs: Supervised mutational signatures

Description

Take a signature representation from SuperSig and group trinucleotides within each feature into interpretable labels, with optional IUPAC labeling from IUPAC_CODE_MAP in the Biostrings package

Usage

simplify_signature(object, iupac)

Arguments

object	an object of class SuperSig
iupac	logical value indicating whether to use IUPAC labels (iupac = TRUE) or not (iupac = FALSE)

Value

simplify_signature returns a vector of simplified features and their difference in mean mean rates between exposed and unexposed (or average rate if the factor is "age")

Examples

head(example_dt) # use example data from package
input_dt <- make_matrix(example_dt) # convert to correct format
input_dt$IndVar <- c(1, 1, 1, 0, 0) # add IndVar column
supersig <- get_signature(data = input_dt, factor = "Smoking")
simplify_signature(object = supersig, iupac = FALSE)
simplify_signature(object = supersig, iupac = TRUE)

TomasettiLab/supersigs documentation built on Dec. 13, 2021, 12:53 a.m.