forwardAlg: forwardAlg

In shimlab/riboHMM2: Analysis tool for Ribo-seq

Description

forwardAlg performs the forward algorithm on a single trajecture of observed chain x. a (in log scale), where a[k,t] = P(Z[t]=k, x[1:t])

Usage

forwardAlg(x, RNA, trans, alpha, beta, E)

Arguments

x	a vector of observed states
RNA	a 0-1 vector. 1 if next 3-base is stop codon
trans	a vector c(rho_u, rho, delta)
alpha	shape parameter in gamma distribution
beta	rate parameter in gamma distribution
E	a scalar. Normalizing constant for the observed chain x.

Value

A matrix, a (in log scale).

Examples

df <- uORF[[1]]
x=df$x; RNA=df$RNA; trans=df$trans; a=df$v; b=df$v/df$m; E=df$E

la <- forwardAlg(x, RNA, trans, a, b, E)

shimlab/riboHMM2 documentation built on May 19, 2019, 6:23 p.m.