merge_cl: Merge clusters based on pairwise differential expressed...

Description Usage Arguments Value

View source: R/cluster.R

Description

Merge clusters based on pairwise differential expressed genes.

Usage

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merge_cl(norm.dat, cl, rd.dat, de.param = de_param(),
  type = c("undirectional", "directional"), max.cl.size = 300,
  de.method = "limma", de.genes = NULL, return.markers = TRUE,
  verbose = 0)

Arguments

norm.dat

normalized expression data matrix in log transform, using genes as rows, and cells and columns. Users can use log2(FPKM+1) or log2(CPM+1)

cl

A vector of cluster membership with cells as names, and cluster id as values.

rd.dat

Reduced dimensions for cells. Used to determine which clusters are close to each other. Clusters are merged among nearest neighbors first.

de.param

The DE gene criteria. See de_param for details.

type

Determine if the DE gene score threshold should be applied to combined de.score, or de.score for up and down directions separately.

max.cl.size

Sampled cluster size. This is to speed up limma DE gene calculation. Instead of using all cells, we randomly sampled max.cl.size number of cells for testing DE genes.

de.method

Use limma by default. We are still testing "chisq" mode.

Value

A list with cl (cluster membership), de.genes (differentially expressed genes), sc (cluster pairwise de.score), markers (top cluster pairwise markers)


AllenInstitute/scrattch.hicat documentation built on Nov. 6, 2018, 9:47 p.m.