Get_for_integrated: To get seurat.obj for integrated

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

To get seurat.obj for integrated

Usage

Get_for_integrated(
  object,
  minfeature = 200,
  mincell = 10,
  species = c("h", "m"),
  minFeatureRNA = NULL,
  maxFeatureRNA = NULL,
  is.tumor = F,
  Percent.mt = NULL,
  projectname = NULL
)

Arguments

object	gene expression matrix
minfeature	Include genes where at least this many features are detected.
mincell	Include cells where at least this many features are detected.
species	the species of the matrix
minFeatureRNA	the min cut off the genes count
maxFeatureRNA	the max cut off the genes count
is.tumor	whether the sample is tumor
Percent.mt	the max cut off of the percetnage of the mitochondrial gene
projectname	the name of the project

Value

the seurat.obj

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_small.csv',package = 'LIANLABDATA')
pbmc_small <- read.csv(input.file, header = T, row.names = 1)

seurat.obj = CreateSeuratObject(counts = pbmc_small, min.features = 200,min.cells = 10)
dim(Abseq.seurat)
See_mRNA(Abseq.seurat)
data[["percent.mt"]] <- PercentageFeatureSet(Abseq.seurat, pattern = "^MT.")  # MT(human)/mt(mouse)
VlnPlot(Abseq.seurat, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
table(Abseq.seurat[["percent.mt"]]<10)

seurat.obj = Get_for_integrated(pbmc_small, minfeature = 200, mincell = 10, species = 'h')

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.