JingXieMIZZOU/hmmASE: Detection of Differentially Allelic Expressed Regions (DAERs) by a Bayesian Hidden Markov Model

Detect the regions or SNPs where the allele specific expression differs for normal and abnormal groups. Depending on the if there exhibits allelic specific expression in the normal group, and whether if the allelic preference for two groups are different, there would be 9 possible states, i.e., B-Neutral, B-Hyper, B-hypo, M-Neutral, M-Hyper, M-hypo, P-Neutral, P-Hyper, P-hypo, for each SNP. The common assupmption of the indepedence between SNPs is not realistic and is too simplistic to understand the complexity of the data. The hmmASE method is based on a bayesian hidden markov model thus can take into account the correlation between adjecent SNPs and gives a more accurate inference about the hidden states of each SNP.

install.packages("remotes")
remotes::install_github("JingXieMIZZOU/hmmASE")