BASiCS (version 0.3.1)

newBASiCS_Chain: Creates a BASiCS_Chain object from pre-computed MCMC chains

Description

BASiCS_Chain creates a BASiCS_Chain-class object from pre-computed MCMC chains.

Usage

newBASiCS_Chain(mu, delta, phi, s, nu, theta)

Arguments

mu

MCMC chain for gene-specific expression levels \(\mu[i]\), defined as true input molecules in case of technical genes (matrix with q columns, technical genes located at the end of the matrix, all elements must be positive numbers)

delta

MCMC chain for gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\), biological genes only (matrix with q.bio columns, all elements must be positive numbers)

phi

MCMC chain for cell-specific mRNA content normalising constants \(\phi[j]\) (matrix with n columns, all elements must be positive numbers and the sum of its elements must be equal to n)

s

MCMC chain for cell-specific capture efficiency (or amplification biases if not using UMI based counts) normalising constants \(s[j]\) (matrix with n columns, all elements must be positive numbers)

nu

MCMC chain for cell-specific random effects \(\nu[j]\) (matrix with n columns, all elements must be positive numbers)

theta

MCMC chain for technical variability hyper-parameter \(\theta\) (vector, all elements must be positive)

Value

An object of class BASiCS_Chain-class.

References

Vallejos, Marioni and Richardson (2015). Bayesian Analysis of Single-Cell Sequencing data.

See Also

BASiCS_Chain-class

Examples

# NOT RUN {
# Data = makeExampleBASiCS_Data()
# MCMC_Output <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5,
#                StoreChains = TRUE, StoreDir = getwd(), RunName = "Test")

# ChainMu = as.matrix(read.table("chain_mu_Test.txt"))
# ChainDelta = as.matrix(read.table("chain_delta_Test.txt"))
# ChainPhi = as.matrix(read.table("chain_phi_Test.txt"))
# ChainS = as.matrix(read.table("chain_s_Test.txt"))
# ChainNu = as.matrix(read.table("chain_nu_Test.txt"))#
# ChainTheta = read.table("chain_theta_Test.txt")[,1]

# MCMC_Output_Load <- newBASiCS_Chain(mu = ChainMu, delta = ChainDelta,
#   phi = ChainPhi, s = ChainS, nu = ChainNu, theta = ChainTheta)
# }