initial.guess: Function to estimate initial alpha and beta values based on...

In carinademel/RNAlife: Quantifying kinetic parameters to determine the RNA life cycle

Description

Function to estimate initial alpha and beta values based on the observed counts (closed form solution) Takes into account if there are replicates for labeled samples or not

Usage

initial.guess(N, L, counts, gene.names = rownames(counts), seq.depths,
  cross.cont, conditions = colnames(counts), conditions.labeling)

Arguments

N	number of cells
L	length of features
counts	feature and time specific counts
gene.names	names of features == rownames of count table
seq.depths	sequencing depth estimates for all samples
cross.cont	cross contamination rate estimates for all samples
conditions	vector of time points/treatment of experiment for each sample
conditions.labeling	vector indicating for each sample if it was labeled RNA or total RNA

Value

list of matrices, alpha and beta values for each feature and each time point

Author(s)

Carina Demel

carinademel/RNAlife documentation built on May 13, 2019, 12:43 p.m.