generate_ribo: generate_ribo

In shimlab/riboHMM2: Analysis tool for Ribo-seq

Description

generate_ribo generates a single trajecture of observed chain x.

Usage

generate_ribo(eL, eH, v, E, p1, p2)

Arguments

eL	a vector. Expected lengths of (5U, uE, 5U2, E, 3U).
eH	a vector. Expected heights of (5U, uI, uE, uT, 5U2, I, E, T, 3U). This is the mean parameter in gamma distribution.
v	a vector. Shape parameter in gamma distribution.
E	a scalar. Normalizing constant for the observed chain x.
p1	a scalar. Probability of uORF is translated.
p2	a scalar. Probability of main region is translated.

Value

A list:

• z_base: a vector. Hidden chain z

• z : a vector. Hidden chain z

• x : a vector. Observed chain x

• RNA : a 0-1 vector. 1 if next 3-base is stop codon

• m : a vector. mean parameter in gamma distribution for each state

• v : a vector. Shape parameter in gamma distribution.

• E : a scalar. Normalizing constant for the observed chain x

• p1, p2

Examples

set.seed(2019)
eL <- c(20, 36, 20, 96, 10)
eH <- c(5, 45,30,15, 40,20,10, 45,30,15,
        5, 90,75,30, 60,50,20, 90,75,30, 5)
v <- rep(10,21)
p1=0.8; p2=0.8
E <- 1

ribo <- generate_ribo(eL, eH, v, E, p1,p2)

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