no.dCG.type: Get mutation type (1-4) of non-CpG mutations

In kdkorthauer/MADGiC: Fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver.

Description

Given a sequence of two characters, the function returns the type of mutation: transition from A/T (1), transversion from A/T (2), transition from non-CpG G/C (3), or transversion from non-CpG G/C (4).

Usage

  no.dCG.type(x)

Arguments

x	a character of length two where each character is either "A","T","G", or "C". For example, x could be "AG". 12 possible two-letter codes.

Details

used internally in mut.type.converter

Value

an integer indicator of mutation type, where 1=transition from A/T, 2=transversion from A/T, 3=transition from non-CpG C/G and 4=transversion from non-CpG C/G. For example x="AG" would return 1 (for transition).

Note

This internal function is not intended to be called by the user.

kdkorthauer/MADGiC documentation built on June 13, 2020, 1:35 p.m.