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

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Merge clusters based on pairwise differential expressed genes.

Description

Merge clusters based on pairwise differential expressed genes.

Usage

merge_cl(
  norm.dat,
  cl,
  rd.dat = NULL,
  rd.dat.t = NULL,
  de.param = de_param(),
  merge.type = c("undirectional", "directional"),
  max.cl.size = 300,
  de.method = "limma",
  de.genes = NULL,
  return.markers = FALSE,
  pairBatch = 40,
  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 cell index 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.
rd.dat.t	Transpose of rd.dat
de.param	The DE gene criteria. See de_param for details.
merge.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.
de.genes	If not null, use DE genes computated prevoiusly by DE_genes_pw or DE_genes_pairs to avoid recomputing.
return.markers	If TRUE, compute the DE genes between very pairs of clusters as markers
pairBatch	The number of pairs to be tested for merging in one batch. Avoid compairing many pairs at the same time to reduce memory comsumption. Default 40
sampled	For big dataset, norm.dat may not include all cells from cl. If TRUE, norm.dat is the data matrix for downsampled cells, and no need for further down sampling.

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 Oct. 20, 2023, 6:55 a.m.