LowMACA-class {LowMACA}R Documentation

Class "LowMACA"

Description

LowMACA class object describing the properties of mutations mapped on pfam domains or proteins

Objects from the Class

Objects can be created by calls of the form newLowMACA(genes, pfam).

Constructor

newLowMACA(genes=character_vector , pfam=character_vector)

Slots

arguments

Object of class "list" with 6 elements:

alignment

Object of class "list" with 4 elements:

mutations

Object of class "list" with 3 elements:

entropy

Object of class "list" with 5 elements:

Methods

alignSequences

alignSequences(object = "LowMACA"): ...

bpAll

bpAll(object = "LowMACA"): ...

entropy

entropy(object = "LowMACA"): ...

getMutations

getMutations(object = "LowMACA"): ...

lfm

lfm(object = "LowMACA"): ...

lmPlot

lmPlot(object = "LowMACA"): ...

mapMutations

mapMutations(object = "LowMACA"): ...

nullProfile

signature(object = "LowMACA"): ...

parallelize

parallelize(object = "LowMACA"): ...

parallelize<-

signature(object = "LowMACA"): ...

lmParams

params(x = "LowMACA"): ...

lmParams<-

signature(object = "LowMACA"): ...

protter

protter(object = "LowMACA"): ...

setup

setup(object = "LowMACA"): ...

show

show(object = "LowMACA"): ...

lfmSingleSequence

lfmSingleSequence(object = "LowMACA"): ...

lmPlotSingleSequence

lmPlotSingleSequence(object = "LowMACA"): ...

Author(s)

Stefano de Pretis, Giorgio Melloni

References

LowMACA website

See Also

newLowMACA

Examples

#ANALYSIS OF SOME OF THE PROTEINS THAT SHARE THE HOMEOBOX DOMAIN
#Genes to analyze
Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
  		,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
			,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
			,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
			,"HOXD3","ISL1","ISX","LHX8")
#Pfam to analyze
Pfam <- "PF00046"
#Construct a new LowMACA object
lm <- newLowMACA(genes=Genes , pfam=Pfam)
#Change some parameters
lmParams(lm)[['tumor_type']] <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")
lmParams(lm)[['min_mutation_number']] <- 1
lmParams(lm)[['density_bw']] <- 0
#Run if you have clustalo installed
lm <- setup(lm)
#Calculate staistics
lm <- entropy(lm)
#Retrieve original mutations
lfm(lm)
#Plot
bpAll(lm)
lmPlot(lm)
protter(lm)

[Package LowMACA version 1.22.0 Index]