xSymbol2GeneID: Function to convert gene symbols to entrez geneid

Description Usage Arguments Value Note See Also Examples

View source: R/xSymbol2GeneID.r

Description

xSymbol2GeneID is supposed to convert gene symbols to entrez geneid.

Usage

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xSymbol2GeneID(data, check.symbol.identity = F, details = F, verbose =
T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

data

an input vector containing gene symbols

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

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.

See Also

xEnricherGenes, xSocialiserGenes

Examples

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## 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)

## End(Not run)

XGR documentation built on May 31, 2017, 1:49 a.m.

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