GenerateVEinfos: Generate Standard Data for One Interaction
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

GenerateVEinfos

R Documentation

Generate Standard Data for One Interaction

Description

This function uses detailed informations about one gene pair(return value of GenerateMapDetailOnepairClusters()), to generate standard data with genes and gene pairs stored seperately.

Usage

GenerateVEinfos(
  onepair.gmoc,
  fgenes.remapped.all,
  direction.X.to.Y = NULL,
  if.ignore.location = FALSE
)

Arguments

`onepair.gmoc`	List. Return value of `GenerateMapDetailOnepairClusters`.
`fgenes.remapped.all`	Data.frame. Informations about feature genes(markers), prefer using return value of `DataPrep.RemapClustersMarkers` and similar functions start with `DataPrep.` here.
`direction.X.to.Y`	Options are 'NULL', 'TRUE', 'FALSE'. It selects subset of data based on direction. The 'NULL' will keep 2-way interacting pairs, 'TRUE' keeps the X-to-Y pairs and 'FALSE' keeps the Y-to-X pairs.
`if.ignore.location`	If set TRUE, genes with different locations or types documented will be treated as the same, and only one row information will be reserved.

Details

This function uses actions that are recorded in STRING action database, but only a small part of actions are thoroughly difined in the database. This function is used to generate formatted data structure (with vertices and edges).

In vertices, all gene informations are well recorded, and every gene is given one unique ID.

In edges, it uses unique vertices IDs to contruct the linkes, and records mode and action.effect for every link.

Value

A list.

cluster.name.A&cluster.name.B: cluster names involved.
edges.infos: data.frame that records the edges(the interaction pairs).
vertices.infos: data.frame that records the vertices(the genes).
vertices.apx.type.A: data.frame that records the types(molecular functions) of A in gene pairs formatted as A-B.
vertices.apx.type.B: data.frame that records the types(molecular functions) of B in gene pairs formatted as A-B.