pickRefSeq: Picks a prioritised RefSeq identifier from a list of...

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

Picks a prioritised RefSeq identifier from a list of identifiers

Description

When translating to RefSeq, typically multiple identifiers are returned, referring to different types of products, such as genomic molecule, mature mRNA or the protein, and they can be predicted, properties that can be read from the prefix (https://www.ncbi.nlm.nih.gov/refseq/). E.g. "XM_" is predicted mRNA and "NP_" is a protein. Run ?org.Bt.egREFSEQ.

Usage

pickRefSeq(
  l,
  priorities = c("NP", "XP", "NM", "XM"),
  reduce = c("all", "first", "last")
)

Arguments

l	Vector or list of RefSeqs accessions to pick from. If list given, applies the prioritation to each element in the list.
priorities	Character vector of prioritised prefixes to pick by. Eg. c("NP","NM") returns RefSeqs starting 'NP', and if none found, those starting 'NM'. If no RefSeqs are found according to the priorities, Null is returned, unless the last element in priorities is '*'. Uses grepl, so see these for pattern matching. Default: c('NP','XP','NM','XM')
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.

Value

If vector given, returns vector. If list given, returns list without element where nothing could be picked.

Author(s)

Stefan McKinnon Edwards [e-mail]

Examples

library(org.Bt.eg.db)
symbols <- c("SERPINA1","KERA","CD5")
refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
mRNA <- pickRefSeq(refseq, priorities=c('NM','XM'))
proteins <- pickRefSeq(refseq, priorities=c('NP','XP'))

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