computeInfRV {fishpond}

R Documentation

Compute inferential relative variance (InfRV)

Description

InfRV is used the Swish publication for visualization. This function provides computation of the mean InfRV, a simple statistic that measures inferential uncertainty. It also computes and adds the mean and variance of inferential replicates, which can be useful ahead of plotInfReps. Note that InfRV is not used in the swish statistical method at all, it is just for visualization. See function code for details.

Usage

computeInfRV(y, pc = 5, shift = 0.01, meanVariance, useCounts = FALSE)

Arguments

y	a SummarizedExperiment
pc	a pseudocount parameter for the denominator
shift	a final shift parameter
meanVariance	logical, use pre-computed inferential mean and variance assays instead of counts and computed variance from infReps. If missing, will use pre-computed mean and variance when present
useCounts	logical, whether to use the MLE count matrix for the mean instead of mean of inferential replicates. this argument is for backwards compatability, as previous versions used counts. Default is FALSE

Value

a SummarizedExperiment with meanInfRV in the metadata columns

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