CreateInterCellObject: Analyze interaction network in full view
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

CreateInterCellObject

R Documentation

Analyze interaction network in full view

Description

This function analyzes count and power of interaction pairs among all given clusters.

Usage

CreateInterCellObject(
  DEG.table,
  species,
  add.exprs = FALSE,
  exprs.data = NULL,
  force.write.exprs = FALSE,
  remap.genes = FALSE,
  cluster.split = "~",
  gene.pair.split = "#~#"
)

Arguments

`DEG.table`	A table on differentially expressed genes and their belonging cell clusters.
`species`	InterCellDB supports species in either 'human' or 'mouse'. Other species are not supported to be used for analysis.
`add.exprs`	It decides whether to add gene expression information.
`exprs.data`	It gives the normalized count matrix as expression information.
`force.write.exprs`	If there is column 'Exprs' in parameter `DEG.table`, users should decide whether to overwrite the existed one (set TRUE) or not (set FALSE).
`remap.genes`	This decides whether to use InterCellDB integrated gene database to standardize all genes to get more perfectly matched with protein/gene pairs database. Default is `FALSE`.
`cluster.split`	The letters used to split 2 cell clusters in one interaction. It can also be modified later by using `setClusterSplit` if not decided yet.
`gene.pair.split`	The letters used to split 2 gene partners in one gene pair. It can also be modified later by using `setGenePairSplit` if not decided yet.

Details

The parameter DEG.table is recommended to be generated by Seurat. Other packages are also applicable, if they could handle scRNA-seq data, do cell clustering and do calculation on cluster-specific differentially expressed genes. The input format of DEG.table should be one data.frame with 4 required columns that are named 'cluster', 'gene', 'LogFC', 'PVal'.

cluster: the cell cluster.
gene: differentially expressed genes, which are grouped by their belonging clusters.
LogFC: the fold change of genes.
PVal: the P value for gene being calculated as differentially expressed gene.

Gene expression data can be added when parameter add.exprs is set TRUE. It will be stored in column 'Exprs' and only those genes given in parameter DEG.table[, "gene"] will be perserved.

To represent one interaction, like interaction between 'Myeloid cell' and 'T cell', it will be looked like 'Myeloid cell~T cell' if cluster.split = "~". To represent oen gene pair, like gene pair of IL6 and IL6R, it will be looked like 'IL6-~-IL6R' if gene.pair.split = "-~-".

To avoid program failure, the letters appearing in gene names are not recommended for gene.pair.split, and the letters appearing in cluster names are not recommended for cluster.split. The program will test for those situation but users should keep this in mind.