R: Function to convert gene symbols to entrez geneid

xSymbol2GeneID

R Documentation

Function to convert gene symbols to entrez geneid

Description

xSymbol2GeneID is supposed to convert gene symbols to entrez geneid.

Usage

xSymbol2GeneID(
data,
org = c("human", "mouse"),
check.symbol.identity = FALSE,
details = FALSE,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

`data`	an input vector containing gene symbols
`org`	a character specifying an organism. Currently supported organisms are 'human' and 'mouse'. It can be an object 'EG'
`check.symbol.identity`	logical to indicate whether to match the input data via Synonyms for those unmatchable by official gene symbols. By default, it sets to false
`details`	logical to indicate whether to result in a data frame (in great details). By default, it sets to false
`verbose`	logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
`RData.location`	the characters to tell the location of built-in RData files. See `xRDataLoader` for details
`guid`	a valid (5-character) Global Unique IDentifier for an OSF project. See `xRDataLoader` for details

Value

a vector containing entrez geneid with 'NA' for the unmatched if (details set to false); otherwise, a data frame is returned

Note

If a symbol mapped many times, the one assiged as the "protein-coding" type of gene is preferred.

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 

# a) provide the input Genes of interest (eg 100 randomly chosen human genes)
## load human genes
org.Hs.eg <- xRDataLoader(RData='org.Hs.eg')
Symbol <- as.character(sample(org.Hs.eg$gene_info$Symbol, 100))
Symbol

# b) convert into GeneID
GeneID <- xSymbol2GeneID(Symbol)

# c) convert into a data frame
df <- xSymbol2GeneID(Symbol, details=TRUE)


# advanced use
df <- xSymbol2GeneID(Symbol, org=org.Hs.eg, details=TRUE)

## End(Not run)