Region.Infer: Region Detection

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

Description

A function to find differentially allelic expressed region based on the predicted hidden status of EM algorithm.

Usage

Region.Infer(EM.out, min.length = 0, min.SNP = 1, max.dist = 1e+20)

Arguments

EM.out	A dataframe includes the predicted hidden status and the genomic postion of each SNP as two columns, which can be the first output of function EM() or a larger dataframe provides other informations in addition to the position and predicted states.
min.length	The minimum length of a differentially allelic expressed region.
min.SNP	The minimum number of SNPs in a differentially allelic expressed region.
max.dist	The maximum gap of two consecutive SNPs in a differentially allelic expressed region.

Value

A list contains the following elements:

region

A dataframe contains 6 columns, i.e., region.cnt, region.start, region.end, region.state,num.SNP and length, which means the index of regions, the start and end position of a region, the predicted state of a region, the number of SNPs and the length in bps of a region, respectively.

DAER.res

A dataframe summarize the input data and predicted hidden status.

JingXieMIZZOU/hmmASE documentation built on Dec. 31, 2019, 12:52 a.m.