FetchGeneOI: Fetch Genes of Interest

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

Fetch Genes of Interest

Description

This function is to fetch genes of interest by selecting on subcellular locations, molecular functions and GO terms.

Usage

FetchGeneOI(object, ...)

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

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

FetchGeneOI.default(
  object,
  sel.location = NULL,
  sel.location.score = c(1:5),
  sel.type = NULL,
  sel.merge.type = NULL,
  ret.with.property = TRUE,
  sel.go.terms = NULL,
  go.use.relative = TRUE,
  go.relative.option = "offspring"
)

Arguments

object	A InterCell object or InterCellDBPack object. FetchGeneOI.default gets InterCellDBPack as input.
...	Parameters passed to function FetchGeneOI.default.
sel.location	Use subcellular location of gene product to select gene, and options are listed in ListAllGeneLocation.
sel.location.score	The score of corresponding subcellular location, range from 1 to 5. Consider score = c(4, 5) as high and common usage.
sel.type	Use molecular function of gene product to select gene, and options are listed in ListAllGeneType.
sel.merge.type	The merged types. Comparing to sel.type, it has less options, which are given in ListAllGeneMergeType. See details for help.
ret.with.property	It decides whether the return values are attached with gene properties(location, type, etc).
sel.go.terms	Use GO terms to select gene, and supported options are listed in ListAllGeneGOTerm.
go.use.relative	Decide if the go terms in the related GO term tree are used. See details for help.
go.relative.option	Decide which relation to the selected GO term is used. Options are 'ancestor', 'parents', 'offspring', 'children'. See details for help.

Details

The parameter sel.merge.type is the summary for sel.type. The options in sel.type are originally generated directly from Uniprot, which comprises over 100 types. For the convenience of usage, we summarize those types and gather them to 16 merged types, which comprise the common used types: 'Receptor', 'Cytokine', 'Growth Factor', etc.

GO terms have 3 basic words: 'cellular_component', 'molecular_function', 'biological_process', and all other GO terms are the offspring of one of them. As a result, GO terms form 3 family tree. Use parameter go.use.relative, it can extend one given GO term to all its related GO terms. There are 4 pre-defined options for selecting specific relative group, which are 'ancestor', 'parents', 'offspring', 'children'. The 'parents' and 'children' are selecting the most close GO terms. For example, 'GO:0006955-immune response' is the nearest level above 'GO:0002250-adaptive immune response', and in turn, 'adaptive immune response' is the children of 'immune response'. The 'ancestor' and 'offspring' goes further than 'parents' and 'children'. The 'ancestor' iteratively searches for the 'parents'. Conversely, the 'offspring' iteratively searches for the 'children'. For example, 'immune response' is the parents of 'adaptive immune response', and 'adaptive immune response' is the parents of 'adaptive immune effector response'. Then, 'immune response' is the 'ancestor' of 'adaptive immune effector response'. The 'offspring' goes the same way by propagating 'children'.

Value

Character, the selected genes. Or, a list, with gene property attached.

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