To install the HMTree package first you need to install devtools,roxygen2 and Rcpp
install.packages("devtools") install.packages("Rcpp") library("devtools") library("Rcpp") install_github("shimlab/HMTree") library("HMTree")
For example, you can simulate 1 curve of length 1024 under Poisson model or Normal model using:
curve.length = 1024 model.mode = 'Poisson' num.samples=1 set.seed(666) res.pois = simu.curves(curve.length=curve.length, model.mode=model.mode, num.samples=num.samples)
curve.length = 1024 model.mode = 'Normal' num.samples=1 normal.sigma=0.5 set.seed(666) res.normal = simu.curves(curve.length=curve.length, model.mode=model.mode, num.samples=num.samples, normal.sigma=normal.sigma)
After simulating data, you can get denoised objects by:
denoised.normal<-HMTree.denoise_1D(res.normal) denoised.pois<-HMTree.denoise_1D(res.pois)
Load output data from Or's code:
local.path<-"/Users/haosicheng/Desktop/" path<-paste0(local.path,"HMTree/docs/output") #Normal path_normal_wavelet_coef<-paste0(path,"/hmt_1024_normal.wavelets_coef.txt") normal_wavelet_coef <- read.table(path_normal_wavelet_coef,col.names = 1, quote="\"", comment.char="") path_normal_denoised_wavelt_coef<-paste0(path,"/hmt_1024_normal_denoised.wavelets_coef.txt") normal_denoised_wavelet_coef <- read.table(path_normal_denoised_wavelt_coef,col.names = 1, quote="\"", comment.char="") path_normal_denoised<-paste0(path,"/hmt_1024_normal_denoised.txt") normal_denoised <- read.table(path_normal_denoised,col.names = 1, quote="\"", comment.char="") #Poisson path_pois_wavelet_coef<-paste0(path,"/pois_1024.wavelets_coef.txt") pois_wavelet_coef<-read.table(path_pois_wavelet_coef,col.names = 1, quote="\"", comment.char="") path_pois_denoised_wavelt_coef<-paste0(path,"/pois_1024_denoised.wavelets_coef.txt") pois_denoised_wavelet_coef <- read.table(path_pois_denoised_wavelt_coef,col.names = 1, quote="\"", comment.char="") path_pois_denoised<-paste0(path,"/pois_1024_denoised.txt") pois_denoised <- read.table(path_pois_denoised,col.names = 1, quote="\"", comment.char="")
Compare:
#Normal normal.output<-denoised.normal diff.normal.wavelet.coef<-(normal.output$wavelet_coef-normal_wavelet_coef)/normal_wavelet_coef summary(diff.normal.wavelet.coef) diff.normal.denoised.wavelet.coef<-(normal.output$denoised_wavelet_coef-normal_denoised_wavelet_coef)/normal_denoised_wavelet_coef summary(diff.normal.wavelet.coef) diff.normal.denoised<-(normal.output$denoised-normal_denoised)/normal_denoised summary(diff.normal.denoised) #Poisson pois.output<-denoised.pois diff.pois.wavelet.coef<-(pois.output$wavelet_coef-pois_wavelet_coef)/pois_wavelet_coef summary(diff.pois.wavelet.coef) diff.pois.denoised.wavelet.coef<-(pois.output$denoised_wavelet_coef-pois_denoised_wavelet_coef)/pois_denoised_wavelet_coef summary(diff.pois.wavelet.coef) diff.pois.denoised<-(pois.output$denoised-pois_denoised)/pois_denoised summary(diff.pois.denoised)
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