dissimilarity_score: Return dissimilarity (to reference proteome) values for a...
In andrewrech/antigen.garnish: Tumor neoantigen prediction
dissimilarity_score R Documentation
Return dissimilarity (to reference proteome) values for a vector of peptides.
Description
Return dissimilarity (to reference proteome) values for a vector of peptides.
Usage
dissimilarity_score(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).
andrewrech/antigen.garnish documentation built on July 8, 2022, 5:19 p.m.
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| dissimilarity_score | R Documentation |
Return dissimilarity (to reference proteome) values for a vector of peptides.
Description
Return dissimilarity (to reference proteome) values for a vector of peptides.
Usage
dissimilarity_score(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).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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