bp.sim.DD: Creates control and manipulated samples based on Beta-Poisson...

Description Usage Arguments Details Value References Examples

View source: R/bp.sim.DD.R

Description

Creates control samples based on Beta-Poisson (BP) model fits for a single-cell RNA-sequencing data set and manipulated samples based on those control samples for simulations involving BP models

Usage

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bp.sim.DD(DATA,N1,N2,case,degree,seedex)

Arguments

DATA

matrix of single-cell RNA-sequencing expression data with genes in rows and samples (cells) in columns

N1

size of the samples drawn from the control BP models

N2

size of the samples drawn from the manipulated BP models

case

case corresponding to a specific parameter manipulation in the BP model; specifically, case can be one of "DLambda", "DAlpha", "DBeta", "DAlphaBeta" or "DPZ" following the design and the respective descriptive table in Schefzik (2021)

degree

parameter to set the degree of the created difference (low to strong), see Schefzik (2021) for details and the choice of a range of possible values

seedex

seed used for sampling from the fitted BP models to ensure reproducibility

Details

Creates control samples based on BP model fits for a single-cell RNA-sequencing data set and manipulated samples based on those control samples for simulations involving BP models. Details regarding the design of the manipulations can be found in Schefzik (2021). Combines the functions bp.sim.control and bp.sim.manipulated.

Value

A list of two:

References

R. Schefzik (2021). SimBPDD: Simulating differential distributions in Beta-Poisson models, in particular for single-cell RNA-sequencing data. Annales Mathematicae et Informaticae, 53:283-298. Available at https://ami.uni-eszterhazy.hu/uploads/papers/finalpdf/AMI_53_from283to298.pdf
T. N. Vu, Q. F. Wills, K. R. Kalari, N. Niu, L. Wang, M. Rantalainen, and Y. Pawitan (2016). Beta-Poisson model for single-cell RNA seq data analyses. Bioinformatics, 32:2128-2135.

Examples

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N1<-500
N2<-500
degree<-1/3
seedex<-24
bp1<-bp.sim.DD(DATA.EX,N1,N2,case="DLambda",degree,seedex)
bp2<-bp.sim.DD(DATA.EX,N1,N2,case="DAlpha",degree,seedex)
bp3<-bp.sim.DD(DATA.EX,N1,N2,case="DBeta",degree,seedex)
bp4<-bp.sim.DD(DATA.EX,N1,N2,case="DAlphaBeta",degree,seedex)
bp5<-bp.sim.DD(DATA.EX,N1,N2,case="DPZ",degree,seedex)

RomanSchefzik/SimBPDD documentation built on May 24, 2021, 1:28 a.m.