run.Seurat3: Wraper for running Seurat3 pipeline

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

Wraper for running Seurat3 pipeline

Description

Wraper for running Seurat3 pipeline

Usage

run.Seurat3(
  seu,
  sce,
  out.prefix,
  gene.exclude.df,
  n.top = 1500,
  measurement = "counts",
  platform = "10X",
  opt.res = "1",
  use.sctransform = F,
  aid = "PRJ",
  plot.rd = c("umap"),
  opt.npc = 15,
  ncores = 16,
  cor.var = c("S.Score", "G2M.Score", "DIG.Score1", "percent.mito", "batchV"),
  ncell.deg = 1500,
  do.deg = F,
  do.scale = F,
  use.harmony = F,
  method.integration = NULL,
  specie = "human",
  gene.mapping.table = NULL,
  res.addition = NULL,
  run.stage = 100
)

Arguments

seu	object of Seurat
sce	object of SingleCellExperiment
out.prefix	character; output prefix
gene.exclude.df	data.frame; gene blak list. Required column: seu.id.
n.top	integer; number of top genes. (default: 1500)
measurement	character; "counts", "TPM" or "cpm". (default: "counts")
platform	character; "10X", "SmartSeq2", "InDrop" etc.. (default: "10X")
opt.res	character; optimal resolution (default: "1")
use.sctransform	logical; whether use scTransform method (default: FALSE)
aid	character; an ID (default: "PRJ")
plot.rd	character vector; reducedDimNames used for plots (default: c("umap"))
opt.npc	integer; optimal number of principal componets to use (default: 15)
ncores	integer; number of CPU cores to use (default: 16)
cor.var	character vector; Subset of c("S.Score","G2M.Score","DIG.Score1","ISG.Score1","percent.mito","batchV") or NULL. (default: c("S.Score","G2M.Score","DIG.Score1","percent.mito","batchV")).
ncell.deg	integer; number of cell to downsample. used in the differentially expressed gene analysis. (default: 1500)
do.deg	logical; whether perform the differentially expressed gene analysis. (default: FALSE)
do.scale	logical; whether scale the expression data. (default: FALSE)
use.harmony	logical; whether use the harmony method. (default: FALSE)
method.integration	character; integration method. (default: NULL)
specie	character; specie, one of "human", "mouse". (default: "human")
gene.mapping.table	data.table; used for gene ID conversion. (default: NULL)
res.addition	character vector; additional resolution parameters. Internally, resolutions from 0.1 to 2.4 will be used. (default: NULL)
run.stage	integer; running stage. (default: 100)

Details

run the Seurat3 pipeline

Value

a list contain a Seurat object and a SingleCellExperiment object

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