BUSseqfits_example {BUSseq}

R Documentation

An external example of the output of the BUSseq_MCMC

Description

This data set is a SingleCellExperiment object generated by running the BUSseq_MCMC function on the simulatied data in the "Example" of BUSseq-package.

Usage

BUSseqfits_example

Format

A SingleCellExperiment object.

Details

The simuated read count data consist of two 150-cell batches. In total, 300 genes are measured. Moreover, all cells come from four cell types.

Source

The "Example" of BUSseq-package

References

Song, Fangda, Ga Ming Angus Chan, and Yingying Wei. Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction. Nature communications 11, no. 1 (2020): 1-15.

Examples

library(SingleCellExperiment)
################################
# Set the Synthetic Parameters #
################################
rm(list=ls())
set.seed(1234)
#The number of batches
B<-2

#The number of cells per batch
nb<-c(150,150)

#The total number of cells
N<-sum(nb)

#The number of genes
G<-300

#The number of cell types
K<-4

# the project name
proj <- "demo"

#The first column of gamma.syn denotes the intercept of 
#the logistic regression for dropout events
#The second column of gamma.syn denotes the odds ratios 
#of the logistic regression for dropout events
gamma.syn<-matrix(0,B,2)
gamma.syn[1,]<-c(-1,-0.5)
gamma.syn[2,]<-c(-1,-0.5)

#the log-scale baseline expression levels
alpha.syn<-rep(0,G)
alpha.syn[1:(G*0.2)]<-2

#the cell-type effects 
beta.syn<-matrix(0,G,K)

#the first cell type is regarded as the reference cell type
beta.syn[,1] <- 0

#the effects of the second cell type
beta.syn[1:(G * 0.2),2] <- -2
beta.syn[(G * 0.20 + 1):(G * 0.4),2] <- 2
beta.syn[(G * 0.4 + 1):G,2] <- 0

#the effects of the third cell type
beta.syn[1:(G * 0.2),3]<- -2
beta.syn[(G * 0.2 + 1):(G * 0.4),3] <- 0
beta.syn[(G * 0.4 + 1):(G * 0.6),3] <- 2
beta.syn[(G * 0.6 + 1):G,3] <- 0

#the effects of the forth cell type
beta.syn[1:(G * 0.2),4]<- -2
beta.syn[(G * 0.2 + 1):(G * 0.6),4] <- 0
beta.syn[(G * 0.6 + 1):(G * 0.8),4] <- 2
beta.syn[(G * 0.8 + 1):G,4] <- 0

#the batch effects
nu.syn<-matrix(NA,G,B)

#the first batch is regarded as the reference batch
nu.syn[,1] <- 0

#the effect of the second batch
nu.syn[1:(G * 0.4),2]<-2
nu.syn[(G * 0.4 + 1):(G * 0.8),2]<-1
nu.syn[(G * 0.8 + 1):G,2]<-2

#the cell-specific size factors
delta.syn <- rep(NA, N)

#The frist cell in each bathc is regarded as the reference cell
delta.syn[1:(nb[1] * 0.5)]<-0
delta.syn[(nb[1] * 0.5 + 1):(nb[1] * 0.9)]<-1
delta.syn[(nb[1] * 0.9 + 1):nb[1]]<-2

#the second batch
delta.syn[1:(nb[2] * 0.5) + nb[1]]<-0
delta.syn[(nb[2] * 0.5 + 1):(nb[2] * 0.7) + nb[1]]<-2
delta.syn[(nb[2] * 0.7 + 1):nb[2] + nb[1]]<--1

#the batch-specific and gene-specific overdispersion parameters
phi.syn<-matrix(10,G,B)

#the cell-type proportions in each batch
pi.syn <- matrix(NA,K,B)

#the frist batch
pi.syn[,1]<-c(0.3,0.3,0.2,0.2)

#the second batch
pi.syn[,2]<-c(0.2,0.24,0.2,0.36)


##############################################
# Simulate Latent Varibles and Observed data #
##############################################
#the cell-type indicators of each cell
w<- rep(NA, N)

#the first batch
nw<-nb[1] * pi.syn[,1]
w[1:nb[1]]<- rep(1:4,nw)

#the second batch
nw<-nb[2] * pi.syn[,2]
w[1:nb[2] + nb[1]]<- rep(1:4,nw)

#the indicators for dropout events
z<- matrix(NA, G, N)

#the underlying true expression levels
x <- matrix(NA, G, N)

#the observed expression levels
y <- matrix(NA, G, N)

#the logarithm of mean expreesion level of each gene in each cell
log.mu <- matrix(NA, G, N)

#generate the latent variable and observed data
batch_ind <- rep(1:B, nb)
for(i in 1:N){
  b <- batch_ind[i]
  log.mu[,i] <- alpha.syn + beta.syn[,w[i]] 
  log.mu[,i] <- log.mu[,i] + nu.syn[,b]
  log.mu[,i] <- log.mu[,i] + delta.syn[i]
  
  for(j in 1:G){
    x[j,i]<-rnbinom(1,phi.syn[j,b],
                    mu=exp(log.mu[j,i]))
    logit_pi <- gamma.syn[b,1] + gamma.syn[b,2] * x[j,i]
    
    z[j,i]<-rbinom(1,1,prob = 1/(1+exp(-logit_pi)))
    if(z[j,i]==0){
      y[j,i]<- x[j,i]
    }else{
      y[j,i]<- 0
    }
  }
}

sce <- SingleCellExperiment(assays = list(counts = y),
                colData = DataFrame(Batch_ind = factor(batch_ind)))
BUSseqfits_example <- BUSseq_MCMC(ObservedData = sce, 
                                  seed = 1234, n.cores = 2,
                                  n.celltypes = 4, n.iterations = 500)

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