extrSpeciesAnnot: Extract species annotation

In wrProteo: Proteomics Data Analysis Functions

Extract species annotation

Description

extrSpeciesAnnot identifies species-related annotation (as suffix to identifyers) for data comnining multiple species and returns alternative (short) names. This function also suppresses extra heading or tailing space or punctuation characters. In case multiple tags are found, the last tag is reported and a message of alert may be displayed.

Usage

extrSpeciesAnnot(
  annot,
  spec = c("_CONT", "_HUMAN", "_YEAST", "_ECOLI"),
  shortNa = c("cont", "H", "S", "E"),
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

annot	(character) vector with initial annotation
spec	(character) the tags to be identified
shortNa	(character) the final abbreviation used, order and lengt must fit to argument annot
silent	(logical) suppress messages
debug	(logical) display additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function returns a character vector with single (last of multiple) term if found in argument annot

See Also

grep

Examples

spec <- c("keratin_CONT","AB_HUMAN","CD_YEAST","EF_G_HUMAN","HI_HUMAN_ECOLI","_YEAST_012")
extrSpeciesAnnot(spec) 

wrProteo documentation built on April 12, 2025, 1:16 a.m.