getMutations: Retrieve mutation data for a LowMACA object

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

Description

Exploting the capabilities of the cgdsr package, this method downloads and parse the mutation data of the specified genes in the selected tumor types. It also aggregates and show the frequencies of mutations of every gene in the different tumor types.

Usage

getMutations(object, repos = NULL)

Arguments

object	a LowMACA class object
repos	a data.frame containing mutations for the specified genes in the LowMACA object in case of custom mutation data. Default NULL

Details

With repos=NULL, the method is a wrapper around cgdsr-getMutationData method from package cgdsr-package. The output of the method is moduled by the parameters in lmParams("LowMACA_object"). See lmParams for further information.

Value

An object of class LowMACA is returned with an update in the slot mutations. See lmMutations method.

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmParams cgdsr-getMutationData lmMutations

Examples

#Create an object of class LowMACA
lm <- newLowMACA(pfam="PF12906")
#Change some paramters
#By default, LowMACA retrieve only missense mutations.
#We want all mutations
lmParams(lm)[['mutation_type']] <- 'all'
#By default, LowMACA takes mutations from all the kinds of tumor
#We want just prostate cancer samples
lmParams(lm)[['tumor_type']] <- 'prad'
lm <- getMutations(lm)

gmelloni/LowMACA documentation built on May 24, 2019, 5:03 a.m.