generate_uORF: generate_uORF

In shimlab/riboHMM2: Analysis tool for Ribo-seq

Description

generate_uORF generates a single trajecture of observed chain x.

Usage

generate_uORF(eL, eH, v, E, r)

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.
r	a scalar. Ratio of chians with uORF and non-uORF.

Value

A list:

• 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

• trans: a vector. (rho, rho_u, delta)

• 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

• stp : a vector. (theta_u, theta) transition probability used

Examples

set.seed(2019)
eL <- c(24, 36, 24, 96, 20)
eH <- c(5, 50,35,20, 40,20,10, 50,35,20,
        5, 60,35,10, 55,25,10, 60,35,10, 5)
v <- rep(1000,21)
E <- 10
r <- 1
df <- generate_uORF(eL, eH, v, E, r)
length(df$x)
barplot(df$x, names.arg=df$z)

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