ASE.HMM: Dection of Differentially Allelic Expressed Regions (DAERs)...

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

Description

A function to implement the hmmASE method.

Usage

ASE.HMM(norm.M, norm.P, abnorm.M, abnorm.P, ex.rm = FALSE, cutoff,
  decoding = "Global", rep = c(4, 4), min.length = 0, min.SNP = 1,
  max.dist = 1e+20)

Arguments

norm.M	A dataframe contains the read counts for maternal allele in normal group. The dimension of this dataframe can vary with the number of available biological replicates but the first 4 columns should be Chromosome, GeneID, Gene_name, and Position.
norm.P	A dataframe contains the read counts for paternal allele in normal group, with similar structure with norm.M.
abnorm.M	A dataframe contains the read counts for maternal allele in abnormal group, with similar structure with norm.M and norm.P.
abnorm.P	A dataframe contains the read counts for paternal allele in abnormal group, with similar structure with other three input datasets.
ex.rm	By setting ex.rm=TRUE, the outliers would be removed from the hidden markov model in the EM steps, and the status prediction would be directly carried out based on the sign of observations. Default value is ex.rm=FALSE which means the observations from all the SNPs would used in the prediction of the best sequence of hidden status.
cutoff	If ex.rm=TRUE, only the observations of SNPs which have |O_1|<= cutoff would be included in the hidden markov model. Setting cutoff=7 or larger is equivalent to setting ex.rm=FALSE.
decoding	Specification of the decoding method for Hidden markov model, which can be either "Local" or "Global", with the latter one referring to the Viterbi algorithm. The default is "Global".
rep	A vector indicates the number of biological replicates for normal and abnormal groups with default value being (4,4).
min.length	The minimum length of a differentially allelic expressed region, defaultly set to be 0.
min.SNP	The minimum number of SNPs in a differentially allelic expressed region with a default value of 1.
max.dist	The maximum gap of two consecutive SNPs in a differentially allelic expressed region, and the default value 10^{20}.

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.