PROPER (version 1.4.2)

estParam: estimate simulation parameters from a count table

Description

This function estimate simulation parameters from a count table, which can be used to set simulation scenarios. The parameters estimated include baseline expression, biological variation in the form of dispersion paramter.

Usage

estParam(X,type = c(1,2))

Arguments

X

An ExpressionSet or a matrix, with entries being RNA sequencing counts

type

type=1 estimates with minimal assumption based on sample means and variances for each genes. type=2 uses edgeR package.

Value

A list with following fields:

seqDepth

Estimated sequencing depth for each sample

lmean

A vector of baseline expression rate per gene in log scale, with length nrow(X)

lOD

A vector of log dispersion for each gene, with length nrow(X)

Details

This is a function that allows a user to establish simulation basis from his/her own data set. Type 1 uses simple average count and sample variance to estimate over dispersion, after normalizing by library size for each sample. Estimated dispersion is bounded at minimum 0.001. Type 2 uses edgeR's AveLogCPM as the estiamte for baseline expression and tagwiseDispersion as the estimate for dispersion.

Examples

## Not run: 
# lmu0=rnorm(20000,5,2)
# lOD0=rnorm(20000,-4,1)
# lmu=exp(rnorm(20000*10,lmu0,exp(lOD0)))
# X=matrix(rpois(20000*10,lmu),20000,10)
# param=estParam(X)
# ## End(Not run)