fitAlphaBeta.log.reparam: Estimate best alpha = labeled amount and best beta =...

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

Description

Estimate best alpha = labeled amount and best beta = unlabeled amount of one gene (either for one or multiple samples). Called in estimateAlphaBeta.

Usage

fitAlphaBeta.log.reparam(counts, labeled.samples, total.samples, L, N, epsilon,
  sigma, disp, alpha.initial, beta.initial, maxit = 10000, trace = FALSE,
  logloglik = TRUE, debug = FALSE)

Arguments

counts	observed counts for a gene (in labeled and total fraction)
labeled.samples	index of labeled sample(s) for which alpha and beta should be estimated
total.samples	index of total sample(s) for which alpha and beta should be estimated
L	length of the gene
N	number of cells
epsilon	vector with cross contamination rate values for Labeled and Total fraction
sigma	vector with sequencing depth values in Labeled and Total fraction
disp	vector with gene-specific disperion estimates (alpha) for Labeled and Total sample to be used in Negative Binomial
alpha.initial	initial alpha value
beta.initial	initial beta value
maxit	maximum number of iterations for the optim function
trace	logical; should all steps be reported
logloglik	should log-loglikelihood be used? (might be more stable against outliers)
debug	should debugging modus be used?

Value

output of optim (a list)

Author(s)

Carina Demel

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