helper_transcriptNames_make {act}

Helper: Makes valid names for all transcripts in a corpus

Description

Makes valid names for all transcript objects in a corpus object based on the names passed in 'transcriptNames' parameter. In particular, the functions also corrects names, which have to be non-empty and unique. The following options are performed in the mentioned order.

Usage

helper_transcriptNames_make(
  transcriptNames,
  searchPatterns = character(),
  searchReplacements = character(),
  toUpperCase = FALSE,
  toLowerCase = FALSE,
  trim = FALSE,
  defaultForEmptyNames = "no_name"
)

Arguments

transcriptNames

Vector of character strings; Names of the transcripts to validate.

searchPatterns

Vector of character strings; Search pattern as regular expression. Leave empty for no search-replace in the names.

searchReplacements

Vector of character strings; Replacements for search. Leave empty for no search-replace in the names.

toUpperCase

Logical; Convert transcript names all to upper case.

toLowerCase

Logical; Convert transcript names all to lower case.

trim

Logical; Remove leading and trailing spaces in names.

defaultForEmptyNames

Character string; Default value for empty transcript names (e.g., resulting from search-replace operations)

Value

List

Examples

library(act)

# make some names with an empty value "" and a duplivate "d"
transcriptNames <- c("a", "b", "", "d", "d")
act::helper_transcriptNames_make(transcriptNames)