SelectDBSubset: Select Subset of Gene Pair Database

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

Select Subset of Gene Pair Database

Description

This function is to select subset of gene pair databases, and options on evidence sources, confidence level, action properties (mode and effect) will be used. The result from different evidence sources will be union in default settings. The result from action properties could be either intersection result or union.

Usage

SelectDBSubset(object, ...)

## S4 method for signature 'InterCellDBPack'
SelectDBSubset(object, ...)

## S4 method for signature 'InterCell'
SelectDBSubset(object, ...)

SelectDBSubset.default(
  object,
  combined.score.range = c(1, 1000),
  use.exp = TRUE,
  exp.score.range = c(1, 1000),
  use.know = TRUE,
  know.score.range = c(1, 1000),
  use.pred = TRUE,
  pred.score.range = c(1, 1000),
  sel.physical = FALSE,
  sel.action.mode = "ALL",
  sel.action.effect = "ALL",
  sel.action.merge.option = "intersect",
  action.score.range = c(1, 1000),
  slim.along.with.pairs = TRUE
)

Arguments

object	A InterCellDBPack or InterCell object. SelectDBSubset.default uses InterCellDBPack as input.
...	Parameters passed to function SelectDBSubset.default.
combined.score.range	The combined score from all evidence sources, which works on the whole database.
use.exp	It adds the data whose evidence is experimentally validatd.
exp.score.range	It controls the score range when selecting subset by experimentally validatd evidence, i.e. when use.exp = TRUE. The score should be 2 numbers within 1~1000.
use.know	It adds the data whose evidence is pathway curated.
know.score.range	It controls the score range when selecting subset by pathway curated evidence, i.e. when use.know = TRUE. The score should be 2 numbers within 1~1000.
use.pred	It adds the data whose evidence is predicted.
pred.score.range	It controls the score range when selecting subset by predicted evidence, i.e. when use.pred = TRUE. The score should be 2 numbers within 1~1000.
sel.physical	It selects the subset of gene pairs whose corresponding protein pairs are physical associated. This parameter is identical to set sel.action.mode = "binding" for now due to the database limitation. It may change in future.
sel.action.mode	Selection by action mode. "ALL" means not use this 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 this 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.
action.score.range	It controls the score range when selecting subset from action databases. The score should be 2 numbers within 1~1000.
slim.along.with.pairs	This decides whether to select the corresponding subset of action pair database after selecting subset of gene pair database.

Details

The 3 evidence channels (use.exp, use.know, use.pred) are in identical priority. For one gene pair, it could have scores from 3 evidence channels at the same time. In default setting, the result of this function will be union of results from 3 channels. If union is not satisfied, the function MergeDBSubset will help.

The score is within 1~1000. Score (>=700) would be consider as high confidence, and (>=900) is even higher confident. Score (>=400) would be consider over medium confidence. Score (<400) would be consider low confidence.

Value

A InterCellDBPack or InterCell object, which is the same as given parameter object.

ZJUDBlab/InterCellDB documentation built on March 19, 2023, 4:56 p.m.