Infer pattern names from region density columns

Scan the region metadata of a qseaSet for columns ending in "_density" (e.g., "CpG_density") and return the base pattern names (e.g., "CpG").

getPattern(qseaSet)

Arguments

qseaSet

qseaSet. Object whose regions (via qsea::getRegions()) may contain *_density columns produced by qsea::addPatternDensity(). Default: none (must be supplied).

Value

character() vector of pattern names discovered (length 0 if none).

Details

This function inspects mcols(qsea::getRegions(qseaSet)), selects column names matching the regex "_density$", and strips that suffix. It does not compute densities or modify the object. If no matching columns exist, a zero-length character vector is returned.

See also

qsea::addPatternDensity(), qsea::getRegions(), S4Vectors::mcols()

Examples

data(exampleTumourNormal, package = "mesa")
# Returns character(0) if no *_density columns are present
exampleTumourNormal %>% getPattern()
#> [1] "CpG"