getMutations {LowMACA} | R Documentation |
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.
getMutations(object, repos = NULL)
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 |
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.
An object of class LowMACA is returned with an update in the slot mutations
.
See lmMutations
method.
Stefano de Pretis , Giorgio Melloni
lmParams
cgdsr-getMutationData
lmMutations
#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)