MethyRegionPlot: Plots methylation data by Genomic Coordinates for a given...

In SpaCCr: Spatial Convex Clustering

Description

Plots methylation data by Genomic Coordinates for a given chromosomal region with cluster means overlayed for each subject.

Usage

MethyRegionPlot(X, Coord, Cluster, SubjInd = 1:3, Start, End)

Arguments

X	A Subject by Probe data matrix for a single chromosome of CNV data
Coord	A vector of Genomic Coordinates for a single chromosome
Cluster	Cluster labels for each probe
SubjInd	A vector of numeric indicies corresponding to the Subjects to be plotted.
Start	Genomic Coordinate minimum
End	Genomic Coordinate maximum

Examples

library(dplyr)
library(tidyr)
data("methy")
methy <- methy[1:20,1:10]
Coordinates <- methy$Genomic_Coordinate
methy %>%
 tbl_df() %>%
 select(-Chromosome,-Genomic_Coordinate) %>%
 gather(Subject,Value,-ProbeID) %>%
 spread(ProbeID,Value) -> X
SubjectLabels <- X$Subject
X <- X[,-1] %>% as.matrix()
nsubj <- nrow(X)
nprobes <- ncol(X)
nweights <- choose(nprobes,2)
diff.vals <- diff(Coordinates)
too.far <- diff.vals > 20000
sig = 1/5e3
w.values <- exp(-sig*diff.vals)
w.values[too.far] = 0

verbose=TRUE
tol.base = 1e-4
tol.miss = 1e-4
max.iter.base=5000
max.iter.miss=500
ngam = 20
gamma.seq <- exp(seq(log(1e-1),log(1e1),length.out=ngam))
CVRes <- SpaCC_CV(X=t(scale(t(X),center=TRUE,scale=FALSE)),
                 w=w.values,
                 gamma.seq=gamma.seq,
                 nfolds=5,
                 nu=1/nsubj,
                 verbose=TRUE,
                 tol.base=tol.base,
                 tol.miss=tol.miss,
                 max.iter.base=max.iter.base,
                 max.iter.miss=max.iter.miss,
                 parallel=FALSE,frac = .1)
PlotCV(CVRes$ErrMat,gamma.seq = CVRes$gamma.seq,rule = 1)
best.gam <- GetGammaCV(CVRes$ErrMat,rule = 1,gamma.seq = CVRes$gamma.seq)
bo <-t(scale(t(X),center=TRUE,scale=FALSE))
bo[is.na(bo)] <- mean(bo,na.rm=TRUE)
Sol <- SpaCC_Missing(t(scale(t(X),center=TRUE,scale=FALSE)),
                        w.values,
                        gamma = best.gam,
                        nu=1/nsubj,
                        verbose=TRUE,
                        tol.base=tol.base,
                        tol.miss=tol.miss,
                        max.iter.base=max.iter.base,
                        max.iter.miss=max.iter.miss,
                        bo,
                        t(diff(t(bo))),
                        t(diff(t(bo))))
VThreshed <- Sol$V
clustsThreshed <- GetClusters(VThreshed)
NEstRegion <- length(unique(clustsThreshed$cluster))
NEstRegion
VThreshed <- ThreshV(Sol$V,X,mult = 1)
clustsThreshed <- GetClusters(VThreshed)
NEstRegion <- length(unique(clustsThreshed$cluster))
NEstRegion
start.coord <- 2e5
end.coord <- 4e5
MethyRegionPlot(X,Coordinates,clustsThreshed$cluster,SubjInd = 1:3,Start=start.coord,End=end.coord)

SpaCCr documentation built on May 2, 2019, 11:02 a.m.