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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 ".bulk.NB.RNAseq_counts" #37

Closed DavidKLim closed 4 years ago

DavidKLim commented 4 years ago

Hi. I am trying out the package to simulate some data, and I was able to estimate parameters fine according to pre-normalized data I have "norm_y". However, it seems like the "simulateCounts()" function is giving me the following error:

Error in .bulk.NB.RNAseq_counts(sim.options = simOptions, phenotype = phenotype, : could not find function ".bulk.NB.RNAseq_counts"

I basically followed the manual line by line, and i'm wondering if this function has been deleted from this package? Please advise. Thank you! Below is what I ran:

estparam <- estimateParam(countData = norm_y, Distribution = 'NB', Protocol = 'Read', RNAseq = 'bulk', Normalisation = 'none')

p.foo <- function(x) mvtnorm::rmvnorm(x, mean=c(4,2,1), sigma = matrix(c(4,2,2,2,3,2, 2, 2, 5), ncol=3))

b.foo <- function(x) rnorm(x, mean=0, sd=1.5)

sim.dat=simulateCounts(n=c(100,110,90), Thinning = NULL, ngenes=10000, p.DE=0.05, pLFC=p.foo, p.B=0.1, bLFC=b.foo, bPattern="uncorrelated", p.M=NULL, mLFC=NULL, params=estparam, LibSize='equal', spikeIns = FALSE, spike = NULL, thinSpike = FALSE, ActualMeans=FALSE, FillUp=FALSE, sim.seed=3, verbose=TRUE)

bvieth commented 4 years ago

Dear Davind,

I am sorry for the inconvenience. While changing a lot for single cell power analysis in powsimR, I forgot to keeop track of the bulk options. In the new version (1.2.0), this should be resolved.

Kind regards Beate