pagoda.reduce.loading.redundancy: Collapse aspects driven by the same combinations of genes

In hms-dbmi/scde: Single Cell Differential Expression

Collapse aspects driven by the same combinations of genes

Description

Examines PC loading vectors underlying the identified aspects and clusters aspects based on a product of loading and score correlation (raised to corr.power). Clusters of aspects driven by the same genes are determined based on the distance.threshold and collapsed.

Usage

pagoda.reduce.loading.redundancy(tam, pwpca, clpca = NULL, plot = FALSE,
  cluster.method = "complete", distance.threshold = 0.01, corr.power = 4,
  n.cores = detectCores(), abs = TRUE, ...)

Arguments

tam	output of pagoda.top.aspects()
pwpca	output of pagoda.pathway.wPCA()
clpca	output of pagoda.gene.clusters() (optional)
plot	whether to plot the resulting clustering
cluster.method	one of the standard clustering methods to be used (fastcluster::hclust is used if available or stats::hclust)
distance.threshold	similarity threshold for grouping interdependent aspects
corr.power	power to which the product of loading and score correlation is raised
n.cores	number of cores to use during processing
abs	Boolean of whether to use absolute correlation
...	additional arguments are passed to the pagoda.view.aspects() method during plotting

Value

a list structure analogous to that returned by pagoda.top.aspects(), but with addition of a $cnam element containing a list of aspects summarized by each row of the new (reduced) $xv and $xvw

Examples

data(pollen)
cd <- clean.counts(pollen)

knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=10, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
varinfo <- pagoda.varnorm(knn, counts = cd, trim = 3/ncol(cd), max.adj.var = 5, n.cores = 1, plot = FALSE)
pwpca <- pagoda.pathway.wPCA(varinfo, go.env, n.components=1, n.cores=10, n.internal.shuffles=50)
tam <- pagoda.top.aspects(pwpca, return.table = TRUE, plot=FALSE, z.score=1.96)  # top aspects based on GO only
tamr <- pagoda.reduce.loading.redundancy(tam, pwpca)

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.