permMclustCov {scDD} | R Documentation

## permMclustCov

### Description

Function to obtain bayes factor for permutations of one gene's residuals

### Usage

    permMclustCov(y, nperms, C, condition, remove.zeroes = TRUE,
      log.transf = TRUE, restrict = FALSE, alpha, m0, s0, a0, b0, ref, min.size)

### Arguments

`y` | Numeric data vector for one gene
`nperms` | Number of permutations of residuals to evaulate
`C` | Matrix of confounder variables, where there is one row for each sample and one column for each covariate.
`condition` | Vector of condition indicators for each sample
`remove.zeroes` | Logical indicating whether zeroes need to be removed from `y`
`log.transf` | Logical indicating whether the data is in the raw scale (if so, will be log-transformed)
`restrict` | Logical indicating whether to perform restricted Mclust clustering where close-together clusters are joined.
`alpha` | Value for the Dirichlet concentration parameter
`m0` | Prior mean value for generating distribution of cluster means
`s0` | Prior precision value for generating distribution of cluster means
`a0` | Prior shape parameter value for the generating distribution of cluster precision
`b0` | Prior scale parameter value for the generating distribution of cluster precision
`ref` | one of two possible values in condition; represents the referent category.
`min.size` | a positive integer that specifies the minimum size of a cluster (number of cells) for it to be used during the classification step. Any clusters containing fewer than `min.size` cells will be considered an outlier cluster and ignored in the classfication algorithm. The default value is three.

### Details

Obtains bayes factor numerator for data vector `y` representing one gene

### Value

Bayes factor numerator for the current permutation

### References

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y

[Package scDD version 1.16.0 Index]