computeInfRV {fishpond} | R Documentation |
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.
computeInfRV(y, pc = 5, shift = 0.01, meanVariance, useCounts = FALSE)
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 |
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 |
a SummarizedExperiment with meanInfRV
in the metadata columns