convDfBeIds: Add BE ID conversion to a data frame

In patzaw/BED: Biological Entity Dictionary (BED)

Add BE ID conversion to a data frame

Description

Add BE ID conversion to a data frame

Usage

convDfBeIds(df, idCol = NULL, entity = FALSE, ...)

Arguments

df	the data.frame to be converted
idCol	the column in which ID to convert are. If NULL (default) the row names are taken.
entity	if TRUE returns BE instead of BEID (default: FALSE). BE CAREFUL, THIS INTERNAL ID IS NOT STABLE AND CANNOT BE USED AS A REFERENCE. This internal identifier is useful to avoid biases related to identifier redundancy. See ../doc/BED.html#3_managing_identifiers
...	params for the convBeIds function

Value

A data.frame with converted IDs. Scope ("be", "source", "organism" and "entity" (see Arguments)) is provided as a named list in the "scope" attributes: attr(x, "scope").

See Also

convBeIds, convBeIdLists

Examples

## Not run: 
toConv <- data.frame(a=1:2, b=3:4)
rownames(toConv) <- c("10", "100")
convDfBeIds(
   df=toConv,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to.source="Ens_gene"
)

## End(Not run)

patzaw/BED documentation built on April 14, 2024, 10:46 p.m.