MakeSeuObj_FromNormalizedRNAData: MakeSeuObj_FromNormalizedRNAData

In yuanqingyan/singleGEO: Query and Analysis of High-throughput Single Cell Sequencing Data from GEO

MakeSeuObj_FromNormalizedRNAData

Description

Make Seurat object from the normalized data which were downloaded from GEO database. To use this function, a list containing the normalized data should be provided. This function is re-written from Seurat package.

Usage

MakeSeuObj_FromNormalizedRNAData(
  NormList = NormList,
  GSE.ID = "Test",
  Frow.which.Norm = "lognorm",
  Feature.selection.method = "vst",
  Nfeatures = 2000,
  Do.scale = TRUE,
  Do.center = TRUE,
  Resolution = 0.8,
  Algorithm = 1,
  Dims = 1:30
)

Arguments

NormList	A list containing the normalized data. Each element of the list is for one normalized dataset. The name of the element will be used as the ID of the normalized dataset. Required.
GSE.ID	The GSE ID for this project. Default: Test
Frow.which.Norm	Which normalization method the data are obtained. Two normalization methods are allowed and supported: lognorm (For LogNormalization) and sct(For sctransform). Default: lognorm
Feature.selection.method	The method for the top variable feature selection. This will feed to FindVariableFeatures function. Default: vst
Nfeatures	The number of top variable features for the FindVariableFeatures function. Default: 2000
Do.scale	Whether to scale the data or not. Binary data. This will feed to ScaleData function. Default: TRUE
Do.center	Whether to center the data or not. Binary data. This will feed to ScaleData function. Default: TRUE
Resolution	The resolution value for FindClusters function. Default: 0.8
Algorithm	The algorithm to be used in FindClusters. Default: 1
Dims	The number of top dimensions of reduction to use for the functions of FindNeighbors and RunUMAP. Default: 1:30

Value

A list with each element corresponding to a Seurat object of a normalized data. The object is ready for the downstream analysis by Seurat package.

Examples

library(singleGEO)

#
data(Norm_GSE134174)
seu_Norm_GSE134174<-MakeSeuObj_FromNormalizedRNAData(NormList=Norm_GSE134174,GSE.ID="GSE134174")

yuanqingyan/singleGEO documentation built on Jan. 11, 2025, 6:35 p.m.