mergeDataFromFileTable: merge data file file table

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

merge data file file table

Description

merge data file file table

Usage

mergeDataFromFileTable(
  exp.list.table,
  gene.de.common,
  seu.list,
  sce.list,
  res.hi,
  method.clustering = "louvain",
  ncores = 12,
  cor.var = c("S.Score", "G2M.Score", "DIG.Score1"),
  contamination.vec = NULL,
  use.harmony = F
)

Arguments

exp.list.table	data.table; one line for a dataset
gene.de.common	character vector; common genes across multiple datasets
seu.list	list; list containing seu objects
sce.list	list; list containing sce objects
res.hi	integer; high resolution used for mini-clusters identification
method.clustering	character; clustering method for mini-clusters identification. (default: "louvain")
ncores	integer; number of CPU cores to use. (default: 12)
cor.var	character vector; subset of c("S.Score","G2M.Score","DIG.Score1","ISG.Score1","score.MALAT1")
contamination.vec	character vector; cells to be excluded. (default: NULL)
use.harmony	logical; use harmony to correct for batch effect (batches are defined in column batchV). (default: FALSE)

Details

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

Value

a list containing 3 components: dat.avg, meta.extra.tb and clust

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