xSymbol2GeneID: Function to convert gene symbols to entrez geneid

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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.

See Also

xRDataLoader

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)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.