library(mulcal)
library(kmerhmm)
fastaFile<-"~/Dropbox/UTX-Alex/jan/combined.fasta"
fastaFile<-"~/Dropbox/UTX-Alex/jan/combined.fasta"
heightFile<-"~/Dropbox/UTX-Alex/jan/combined_heights.bed"
temp<-read.table(heightFile)
data<-as.matrix(temp[,4:dim(temp)[2]])
dataLocs<-list(list("eryt", 1, "top"),
list("tall", 1,"bottom"),
list("ecfc",3,"top"),
list("other",c(3,5),c("top","top")),
list("meka",c(3,7),c("top","top")),
list("hspc",c(3,7),c("top","bottom")),
list("diff", 7, "top"))
normData<-qn(data)
prc<-prcomp(t(normData))$rotation
mers<-countNMers(fastaFile,prc[,1],8)
wei2<-mers[,2]
names(wei2)<-as.character(mers[,1])
medWei<-median(wei2)
MAD<-median(abs(wei2-medWei))
sigma=4*MAD/0.6745
erythroid<-sort(wei2[wei2>sigma])
leukemic<-sort(wei2[wei2<(-sigma)])
library(msa)
library(abind)
msaResults<-msa(names(leukemic),"Muscle",cluster="neighborjoining",gapOpening = 420, gapExtension =10,type="dna")
consensusString(msaResults)
levels<-c("A","C","G","T","-")
nodes<-30
iterations<-5
#starts<-10
sequences<-as.matrix(msa(names(leukemic),type="dna"))
hmm<-buildHMM(sequences,levels,nodes)
C2DD<-function(n,dim,varname){
paste("const double",varname, "[][]= {{",paste(apply(matrix(runif(n*dim),ncol=dim),2,function(x) paste(x/sum(x),collapse=", " )),collapse ="},{"),"}};\n")
}
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