wrProteo: extrSpeciesAnnot – R documentation

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extrSpeciesAnnot

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,
  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
`callFrom`	(character) allows easier tracking of messages produced

Value

character vector with single (last of multiple) term if found in argument annot

Examples

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

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release