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Cleanup Genomic Contexts

Source: R/cleanup.R
cleanup_gencontext.Rd

Cleans up the GenContext column of a data frame by removing certain characters and rows.

This function removes empty rows based on the 'GenContext' column. A cleaned up version of the data table is returned.

Usage

cleanup_gencontext(
  prot,
  domains_rename = data.frame(old = character(0), new = character(0), stringsAsFactors =
    F),
  repeat2s = TRUE,
  remove_asterisk = TRUE
)

Arguments

prot

A data frame that contains columns 'GenContext.orig'

domains_rename

A data frame containing the domain names to be replaced in a column 'old' and the replacement in a column 'new'. Defaults to an empty data frame with a new and old column such that non of the domains will be renamed

repeat2s

Boolean. If TRUE, repeated domains in 'GenContext' are condensed. Default is TRUE.

remove_asterisk

Boolean. If TRUE, asterisks in 'ClustName' are removed. Default is TRUE.

Value

A cleaned up version of the data table is returned.

Examples

if (FALSE) { # \dontrun{
cleanup_gencontext(prot, domains_rename, T, F)
} # }