Return dissimilarity (to reference proteome) values for a vector of nmers.

garnish_dissimilarity(v, db, kval = 4.86936, aval = 32)

Arguments

v

Character. Vector of nmers.

db

Character. One of c("mouse", "human").

kval

Numeric. Steepness of sigmoidal curve at k. Default 4.86936, the value used in the analysis of Van Allen, Snyder, Rizvi, Riaz, and Hellmann datasets.

aval

Numeric. Optionally can be "mean" to use mean alignment for nmers passed. Horizontal displacement of partition function. Default is 32, based on max_SW of 75 million 8-15mers from the five clinical datasets against human, if using max_SW, use 52. This value may not be meaningful for murine alignment so use with care.

Value

Data table of nmers and corresponding dissimilarity values (to the non-mutated proteome).