permMclustCov: permMclustCov

View source: R/permutations.R

permMclustCovR 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


kdkorthauer/scDD documentation built on March 27, 2022, 5:11 a.m.