estParam {PROPER} | R Documentation |
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.
estParam(X,type = c(1,2))
X |
An ExpressionSet or a matrix, with entries being RNA sequencing counts |
type |
|
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.
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 |
lOD |
A vector of log dispersion for each gene, with length |
Jean Wu <zhijin_wu@brown.edu>
## 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)