Get_Keyword_Meta: Get_Keyword_Meta

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

Get_Keyword_Meta

Description

Filter the meta database to obtain the study using single cell RNAseq data and containing the key information provided by user

Usage

Get_Keyword_Meta(
  GeoDataBase = GeoDataBase,
  Organism = "Homo sapiens",
  InputSearchList = list(kw1 = "single"),
  Platform = "scRNAseq"
)

Arguments

GeoDataBase	The object returned by getGeoMetaDatabase function. Required
Organism	The organisms to search for. One or multiple organisms can be provided. Optional. Default: c("Homo sapiens")
InputSearchList	The list of keywords which are described in GEO database. Multiple keywords can be provided and the keywords should be in a list. Required. Default: c("single")
Platform	The platform of single cell sequencing. Currently only support single cell RNAseq(scRNAseq) and single cell ATACseq(scATACseq). Options: scRNAseq, scATACseq. Default: "scRNAseq"

Value

The filtered meta data

Examples

library(singleGEO)
MyDataBase<-GetGeoMetaDatabase(Sqlfile=NULL,Demo=TRUE)
MyOrganism<-c("Mus musculus","Homo sapiens")
search_kw1<-c("lung","pulmonary")
search_kw2<-c("fibrosis")
KeyList<-list(kw1=search_kw1,kw2=search_kw2)
MySearch<-Get_Keyword_Meta(GeoDataBase=MyDataBase,Organism=MyOrganism, InputSearchList=KeyList)

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