InterCell-class: The InterCell Class
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

InterCell-class

R Documentation

The InterCell Class

Description

The InterCell object is used to in all the analysis InterCellDB provided. It incoporates the necessary databases, and stores every important intermediate result.

Slots

fgenes: InterCellDB needs the differential expressed genes and their belonging clusters as input. The given data need to have columns named 'gene', 'cluster', 'LogFC', 'PVal'. Those each means, 'gene': the authorized gene names, 'cluster': cell cluster, 'LogFC': the log transformed fold change of genes, 'PVal': the P val for regarding one gene as differentially expressed one. The expression level of each gene is also needed when statistical test is required and it should be stored in column named 'Exprs'.
database: Database stored in InterCellDBPack object.
formulae: The default formulae to be used in analysis.
inter.fullview: This is used to store the result of network analysis.
tg.itinfo: This stores information about one intercellular communication.
tg.action.pairs: This is used to store the intermediate result of action properties and gene pairs.
tg.veinfo: This is used to store the intermediate result of one intercellular communication (for one interacting 2-cell group).
tg.action.comp: This is used to store the result of analyzing composition of action mode and action effect in one interacellular communication.
tg.spgenes: This is used to store the selected gene pairs and all their participating interacitons in one intercellular communication.
tool.vars: This stores several variables to be used embedded in program.
misc: The not important intermediate result will be put in this parameter as well as some pre-defined settings.