rbonneville
commented
6 years ago Hello @twelvesummer ,
These default values are for thresholds to classify a sample as MSI-H (microsatellite instability-high). Although the code provides three distance metrics for comparing microsatellite length distributions, we recommend the DIF metric (default threshold 0.4).
With this recommended metric and default settings, a tumor's (versus its matched normal) MSI score will fall within [0.0, 2.0], and tumors with score >=0.4 are called MSI-H.
hello,I have read this script from a paper named "Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS" which writed "Once the scores for each locus are assigned,the average of all the locus instability scores is calculated,to provide a single numerical value representing the average aggregate instability present in the sample. Scores reported range from 0.0 (entirely stable) to 2.0 (entirelyunstable).". However,I find mantis.py that the default value isn't the same,which one above? Parameter(key='dif_threshold', default=0.4), Parameter(key='euc_threshold', default=0.187), Parameter(key='cos_threshold', default=0.07),