SearchGene: Function to search for functionally similar genes
In FSim: A package to search functionally similar genes

Description Usage Arguments Value Author(s) See Also Examples

View source: R/SearchTerm.R

For interested gene or a group of GO terms, the function can be used to search for functionally similar genes in a target gene list or all GO annotated genes.

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SearchGene(gene = NULL, symbol = NULL, terms = NULL, targets = "ALL", n
= 50, an.go, ontology = "ALL", term2ancestor = TRUE, map =
"org.Hs.eg.db", plot = FALSE)

`gene`	The input gene id for searching functionally similar gene list.
`symbol`	The input gene symbol for searching gene list.
`terms`	The input GO terms for searching gene list.
`targets`	The searched gene list. It can be a group of gene IDs or "ALL". "ALL" means to search for the most related gene list in all GO annotated genes.
`n`	If targets is "ALL", n is the amount of target genes based on the number of shared GO terms between input gene and target genes in decreasing order.
`an.go`	The R enviroment that provide mappings between gene IDs and GO IDs including their ancestors.
`ontology`	The GO ontology to use in the search. It can be "BP", "MF", "CC" and "ALL" for the three ontologies.
`term2ancestor`	The option works when terms is not NULL. If TRUE, the input term and their ancestor terms will be used. If FALSE, the input term will be used directly.
`map`	The GO annotation package.
`plot`	If TRUE, a heatmap will be plotted to show the shared GO terms.

A data.frame object including functionally similar genes. The columns are

`Symbol`	The gene symbol of similar genes.
`sharedTerms`	The number of shared GO terms between input gene and similar genes.
`value`	The kappa value between input gene and returned gene.
`ASE`	The Approximate Standard Error for the kappa value.
`z.value`	The Z score to standardize the kappa value.