BASiCS_CorrectOffset: Remove global mean expression offset

In BASiCS: Bayesian Analysis of Single-Cell Sequencing data

Description

Remove global offset in mean expression between two BASiCS_Chain objects.

Usage

BASiCS_CorrectOffset(Chain, ChainRef, min.mean = 1)

Arguments

Chain	a 'BASiCS_MCMC' object to which the offset correction should be applied (with respect to 'ChainRef').
ChainRef	a 'BASiCS_MCMC' object to be used as the reference in the offset correction procedure.
min.mean	Minimum mean expression threshold required for inclusion in offset calculation. Similar to 'min.mean' in 'scran::computeSumFactors'.

Value

A list whose first element is an offset corrected version of 'Chain' (using 'ChainRef' as a reference), whose second element is the point estimate for the offset and whose third element contains iteration-specific offsets.

Author(s)

Catalina A. Vallejos [e-mail]

Nils Eling [e-mail]

Alan O'Callaghan

Examples

# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data(ChainSC)
data(ChainRNA)

A <- BASiCS_CorrectOffset(ChainSC, ChainRNA)

# Offset corrected versions for ChainSC (with respect to ChainRNA). 
A$Chain
A$Offset

BASiCS documentation built on April 16, 2021, 6 p.m.