add threshold = "cut" back

[dimalvovs]

• add threshold="cut" back
• make best inclusion rank < and not <= first rank where intra-pattern becomes worse than inter-pattern;
• create tests
• update documentation

[jmitchell81]

The improvement of roxygen2 documentation for the patternMarkers function is greatly appreciated. The approach to thresholding based on the inter-pattern ranking of the feature is implemented clearly and efficiently. Unit tests are effective at ensuring that capability to detect pattern markers and disregard non-specific features. LGTM