makeInfReps.RdMakes pseudo-inferential replicate counts from
mean and variance assays. The simulated
counts are drawn from a negative binomial distribution,
with mu=mean and size set using a method
of moments estimator for dispersion.
makeInfReps(y, numReps, minDisp = 0.001)a SummarizedExperiment
how many inferential replicates
the minimal dispersion value, set after method of moments estimation from inferential mean and variance
a SummarizedExperiment
Note that these simulated counts only reflect marginal
variance (one transcript or gene at a time),
and do not capture the covariance of counts across
transcripts or genes, unlike imported inferential
replicate data. Therefore, makeInfReps should
not be used with summarizeToGene to create
gene-level inferential replicates if inferential
replicates were originally created on the transcript
level. Instead, import the original inferential
replicates.
Van Buren, S., Sarkar, H., Srivastava, A., Rashid, N.U., Patro, R., Love, M.I. (2020) Compression of quantification uncertainty for scRNA-seq counts. bioRxiv. https://doi.org/10.1101/2020.07.06.189639
library(SummarizedExperiment)
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mean <- matrix(1:4,ncol=2)
variance <- mean
se <- SummarizedExperiment(list(mean=mean, variance=variance))
se <- makeInfReps(se, numReps=50)