SelectInterSubset: Select Some Gene Pairs from One Interaction
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

SelectInterSubset

R Documentation

Select Some Gene Pairs from One Interaction

Description

This function is to further select subset of interacting gene pairs in given interaction

Usage

SelectInterSubset(
  object,
  direction.X.to.Y = NULL,
  sel.exprs.change = c("Xup.Yup", "Xup.Ydn", "Xdn.Yup", "Xdn.Ydn"),
  sel.some.genes.X = NULL,
  sel.some.genes.Y = NULL,
  sel.genes.option = "intersect",
  sel.gene.pairs = NULL,
  sel.action.mode = "ALL",
  sel.action.effect = "ALL",
  sel.action.merge.option = "intersect"
)

Arguments

`object`	A `InterCell` object, which is created by `CreateInterCellObject`.
`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.
`sel.exprs.change`	Options are 'Xup.Yup', 'Xup.Ydn', 'Xdn.Yup', 'Xdn.Ydn'. It gives the corresponding expression change of every interacting gene pair.
`sel.some.genes.X`	It gives the target genes expected to be expressed by cluster X ( the same as parameter `cluster.x` in `FetchInterOI`).
`sel.some.genes.Y`	It gives the target genes expected to be expressed by cluster Y ( the same as parameter `cluster.y` in `FetchInterOI`).
`sel.genes.option`	Options are 'intersect' or 'union'. 'intersect' strictly restricts gene pair to have one gene partner in `sel.some.genes.X` and the other in `sel.some.genes.Y`. 'union' restricts gene pair to have at least one gene either in `sel.some.genes.X` or `sel.some.genes.Y`.
`sel.gene.pairs`	Directly specify the desired gene pairs. It should be given in standard table that is generated by `FormatCustomGenePairs`. The genes in "inter..A" will be applied to cluster X, and "inter..B" will be applied to cluster Y.
`sel.action.mode`	Selection by action mode. "ALL" means not use action mode to select subset. Other options will be directly select gene pair in that action mode. Supported options are listed in `kpred.action.mode`.
`sel.action.effect`	Selection by action effect. "ALL" means not use action effect to select subset. Other options will be directly select gene pair in that action effect. Supported options are listed in `kpred.action.effect`.
`sel.action.merge.option`	Either 'intersect' or 'union'. The option for merging the result from selection on action mode and action effect.