XGR (version 1.1.7)

xSymbol2GeneID: 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 = F,
details = F,
verbose = T,
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

See Also

xEnricherGenes, xSocialiserGenes

Examples

# NOT RUN {
# Load the library
library(XGR)

# 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)
# }