SearchDatabase: Search Pathways in GO/Reactome Database

In huayc09/SeuratExtend: SeuratExtend

Search Pathways in GO/Reactome Database

Description

Search for pathways in the GO or Reactome database using a gene name, pathway ID (SetID), or pathway name (SetName).

Usage

SearchDatabase(
  item,
  type = c("gene", "SetID", "SetName"),
  database = c("GO", "Reactome"),
  spe = getOption("spe"),
  export.to.data.frame = F,
  n.min = 1,
  n.max = Inf,
  only.end.terms = F,
  return = c("all", "ID", "genelist")
)

Arguments

item	A gene name, pathway ID, or pathway name.
type	Types of search criteria. Can be one or a combination of "gene", "SetID", "SetName". Default: c("gene", "SetID", "SetName").
database	The database to search in: "GO", "Reactome", or both. Default: c("GO", "Reactome").
spe	Species, either 'human' or 'mouse'. Default: getOption("spe").
export.to.data.frame	If TRUE, the results will be returned as a data frame, which can be easily exported to csv or xlsx formats. Default: FALSE.
n.min	Minimum number of genes required in the gene set. Default: 1.
n.max	Maximum number of genes allowed in the gene set. Default: Inf.
only.end.terms	If TRUE, only the end-level pathways or gene sets will be returned. Default: FALSE.
return	Specifies the format of the result. If set to "all" (default), the result will include all information (pathway ID, pathway name, genes). If set to "ID", it will only return a vector of pathway IDs. If set to "genelist", it will return a list where the names are pathway IDs and the contents are the corresponding genes.

Details

Further details and usage can be seen in the provided examples.

Value

Depending on the specified parameters, the function returns:

• A full list (with pathway ID, pathway name, and genes) if return = "all".

• A vector of pathway IDs if return = "ID".

• A named list of genes with pathway IDs as the list names if return = "genelist".

• A data frame if export.to.data.frame = TRUE.

Examples

library(SeuratExtend)
library(dplyr)
options(max.print = 10)

# Set the default database search to 'human'
options(spe = "human")

# The 'item' parameter can be anything like a gene, pathway ID, or pathway name.
# For example, search in the GO/Reactome database for pathways that contain the "CD3D" gene
# or pathway names that include "metabolic".
result <- SearchDatabase(c("CD3D","metabolic"))
names(result)
glimpse(head(result, 5))

# If you only want to search based on gene names, you can specify this in the 'type' parameter.
result <- SearchDatabase("CD3D", type = "gene")
names(result)

# If you want to search in a specific database, you can specify it using the 'database' parameter.
result <- SearchDatabase("CD3D", database = "Reactome")
names(result)

# You can specify the database to be either 'human' or 'mouse' using the 'spe' parameter.
result <- SearchDatabase("Cd3d", spe = "mouse")
glimpse(head(result, 5))

# If you only want the result to be a list of pathway IDs, which could be useful for subsequent analysis,
# you can set the 'return' parameter accordingly.
result <- SearchDatabase("CD3D", return = "ID")
result

# If you want the output as a gene list, with the IDs as names, suitable for inputs like GeneSetAnalysis,
# you can adjust the 'return' parameter.
result <- SearchDatabase("CD3D", return = "genelist")
glimpse(head(result, 5))

# If you prefer the output to be a data frame, which is suitable for exporting to Excel or CSV formats,
# you can set 'export.to.data.frame' to TRUE.
result <- SearchDatabase("CD3D", export.to.data.frame = TRUE)
glimpse(result)

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.