uORF: uORF data

In shimlab/riboHMM2: Analysis tool for Ribo-seq

Description

An uORF dataset contains num=500 transcripts generated by generate_uORF with parameters:

• 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)

• E <- c(rep(1,num/5), rep(5,num/5), rep(10,num/5), rep(15,num/5), rep(20,num/5))

• r <- 4

so trans = c(0.04, 0.01, 0.05) and m = eL / E

Usage

uORF

Format

A list with 100 trajectories. Each list has variables as follows:

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

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