lmMutations: Show Mutation Data Contained in a LowMACA object

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Show Mutation Data Contained in a LowMACA object

Description

Method for objects of class LowMACA. It can show the mutation data contained within the LowMACA object that has been retrieved from getMutations method.

Usage

lmMutations(object)

Arguments

object

object of class LowMaca

Value

A list containing the following elements:

• data a data.frame describing the mutations on every genes and their effect the amino acids they belong to

• freq a data.frame containing the absolute number of mutated patients by gene and selected tumor types (this is useful to explore the mutational landscape of your genes in the different tumor types)

• aligned a matrix where rows represent proteins/pfam, and columns report the number of mutations on every position of the consensus

Author(s)

Stefano de Pretis, Giorgio Melloni

See Also

getMutations

Examples

data('lmObj')
str(lmMutations(lmObj))

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.