Get_Seurat: To get seurat.obj easily

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

Description

To get seurat.obj easily

Usage

Get_Seurat(
  object,
  minfeature = 200,
  mincell = 10,
  species = c("h", "m"),
  minFeatureRNA = NULL,
  maxFeatureRNA = NULL,
  Percent.mt = NULL,
  is.tumor = F,
  projectname = NULL,
  dim.FindNeighbors = 1:30,
  dims.TSNE = 1:30
)

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
Percent.mt	the max cut off of the percetnage of the mitochondrial gene
is.tumor	whether the sample is tumor
projectname	the name of the project
dim.FindNeighbors	number of dims to find neighbors
dims.TSNE	number of dims to t-SNE

Value

the seurat.obj including PCA, t-SNE

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_small.csv',package = 'LIANLAB')
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_Seurat(pbmc_small, minfeature = 200, mincell=10,species='h')

## End(Not run)

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