mergeSCEDataFromFileTable: collapse gene by cell expression data to gene by mini-cluster...

In Japrin/scPip: pipeline for scRNA-seq data analysis

collapse gene by cell expression data to gene by mini-cluster expression data, with input stored in SingleCellExperiment object

Description

collapse gene by cell expression data to gene by mini-cluster expression data, with input stored in SingleCellExperiment object

Usage

mergeSCEDataFromFileTable(
  exp.list.table,
  gene.common,
  sce.list,
  group.vec,
  ncores = 6,
  contamination.vec = NULL,
  block.size = 1500
)

Arguments

exp.list.table	data.table; one line for a dataset
gene.common	character vector; common genes across multiple datasets
sce.list	list; list containing sce objects
group.vec	character; cell id to mini-cluster mapping vector
ncores	integer; number of CPU cores to use
contamination.vec	character vector; cells to be excluded. (default: NULL)
block.size	integer; block size. To process large matrix, each time a block of [INT] genes is processed (default: 1500)

Details

For each dataset, the function first identify mini-clusters, then calculate the average expressions of mini-clusters.

Value

a list, each component of which is expression matrix of gene.common by min-clusters

Japrin/scPip documentation built on Jan. 29, 2024, 1:20 a.m.