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
cleanGenomicContext(
prot,
domains_rename = data.frame(old = character(0), new = character(0), stringsAsFactors =
F),
condenseRepeatedDomains = 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
- condenseRepeatedDomains
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.