Computes the number of unique CpG sites (defined by distinct pairs of
start and end positions) in a table of calls within a mod
database. Accepts either a file path to a database or an existing mod
database object.
Arguments
- mod_db
Character string giving the path to a mod database file, or an object/handle accepted by
.modhelper_connectDB().- table_name
Character scalar. Name of the table to query. Defaults to
"calls".
Value
An integer (length-one) giving the number of unique CpG sites,
returned invisibly. If table_name does not exist, returns
NULL invisibly after printing a message. The function also prints a
formatted summary to the console as a side effect.
Errors
If mod_db is a character path and the file does not exist, an error is
thrown with stop() before attempting any connection.
Examples
if (FALSE) { # \dontrun{
# Using a file path
n <- get_mod_cpg_count("/path/to/my.mod.db", table_name = "calls")
n
# Using a pre-opened handle (package-internal)
dbh <- .modhelper_connectDB("/path/to/my.mod.db")
get_mod_cpg_count(dbh) # prints summary, returns value invisibly
} # }