In piotrsobecki/rdmdecon: Deconvolution based on Roadmap data

knitr::opts_chunk$set(echo = TRUE,error=TRUE,warnings=FALSE)

57 Signature deconvolution of roadmap data

library(rdmdeconv)
res <- deconv(epigenomes57.N)
head(res[,1:6])

marker extraction based on 4 proportions

#Make signatures based on 4 proportions
signatures4 = make_signatures(proportions4_fben)

colnames(signatures4)

#Extract markers from signatures
extracted_markers4 = extract_markers(signatures4)
extracted_markers4 <- extracted_markers4[extracted_markers4$padj==0,] # get only markers with 0 padj (lowest)
str(extracted_markers4)
#Show chosen extracted markers
head(data.frame(signatures4[extracted_markers4$id,],extracted_markers4$padj),50)

4 signatures decomposition of roadmap data using different methods and extracted markers

#Deconvolution without markers
res <- deconv(epigenomes57.N,signatures4)
plotRes(res)

#Deconvolution with markers lsfit method
res <- deconv(epigenomes57.N,signatures4,markers=extracted_markers4$id)
plotRes(res)

#Deconvolution with markers lsfit method
res <- deconv(epigenomes57.N,signatures4,markers=extracted_markers4$id)
plotRes(res)

#Deconvolution with markers qprog method
res <- deconv(epigenomes57.N,signatures4,markers=extracted_markers4$id,method = 'qprog')
plotRes(res)

#Deconvolution with markers deconf method
res <- deconv(epigenomes57.N,signatures4,markers=extracted_markers4$id,method = 'deconf')
plotRes(res)