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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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could not find function "insilicoNBParam" #39

Closed taryn0h closed 4 years ago

taryn0h commented 4 years ago

Hi. I'm trying to do some simulation to calculate power for a single cell RNA-seq study. I'm getting hung up with the in silico parameter simulation function.

Just running the example I get this: insilico.singlecell <- insilicoNBParam(means=function(x) rgamma(x, 4, 2), dispersion=function(x) 2 + 150/x, dropout=NULL, sf=function(x) 2^rnorm(n=x, mean=0, sd=0.5), RNAseq='singlecell')

Error in insilicoNBParam(means = function(x) rgamma(x, 4, 2), dispersion = function(x) 2 + : could not find function "insilicoNBParam"

bvieth commented 4 years ago

Hello,

I have removed this functionality from powsimR since we found that using these dispersion functions for simulations was not really realistic for single cells because the variability was too low.

I would recommend to use a publicly available data set, e.g. from conquer or recount2 that resembles the expression data you are interested in and want to do statistical power analysis on.

Kind regards Beate