translate: Translate between different identifiers

In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

Translate between different identifiers

Description

Function for translating from one annotation to another, eg. from RefSeq to Ensemble. This function takes a vector of annotation values and translates first to the primary annotation in the Biocore Data Team package (ie. entrez gene identifier for org.Bt.eg.db) and then to the desired product, while removing non-translated annotations and optionally reducing the result so there is only a one-to-one relation.

Usage

translate(
  values,
  from,
  to = NULL,
  reduce = c("all", "first", "last"),
  return.list = TRUE,
  remove.missing = TRUE,
  simplify = FALSE,
  ...
)

Arguments

values	Vector of annotations that needs translation. Coerced to character vector.
from	Type of annotation values are given in. NB! take care in the orientation of the package, ie. if you have RefSeq annotations, use org.Bt.egREFSEQ2EG or (in some cases) revmap(org.Bt.egREFSEQ).
to	Desired goal, eg. org.Bt.egENSEMBLPROT. If NULL (default), goal if the packages primary annotation (eg. entrez gene for org.Bt.eg.db). Throws a warning if the organisms in from and to are not the same.
reduce	Reducing method, either return all annotations (one-to-many relation) or the first or last found annotation. The reducing step is applied after translating to the goal: all: returns all annotations first or last: choose first or last of arbitrarily ordered list.
return.list	Logical, when TRUE, returns the translation as a list where names
remove.missing	Logical, whether to remove non-translated values, defaults TRUE.
simplify	Logical, unlists the result. Defaults to FALSE. Usefull when using translate in a lapply or sapply.
...	Additional arguments sent to pickGO if from returns GO set.

Details

If you want to do some further mapping on the result, you will have to use either unlist og lapply, where the first returns all the end-products of the first mapping, returning a new list, and the latter produces a list-within-list.

If from returns GO identifiers (e.g. from = org.Bt.egGO), then the returned resultset is more complex and consists of several layers of lists instead of the usual list of character vectors. If to has also been specified, the GO IDs must be extracted (internally) and you have the option of filtering for evidence and category at this point. See pickGO.

Value

List; names of elements are values and the elements are the translated elements, or NULL if not translatable with remove.missing = TRUE.

Note

Requires user to deliver the annotation packages such as org.Bt.egREFSEQ.

Author(s)

Stefan McKinnon Edwards [e-mail]

See Also

pickRefSeq, pickGO

Examples

library(org.Bt.eg.db)
genes <- c(280705, 280706, 100327208)
translate(genes, org.Bt.egSYMBOL)

symbols <- c("SERPINA1","KERA","CD5")
refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
# Pick the proteins:
pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')

# If you wanted do do some further mapping on the result from
# translate, simply use lapply.

library(GO.db)
GO <- translate(genes, org.Bt.egGO)

kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.