Score wt and mt sequences for a pwm
1 2 3 | computeRewiring(obj, mut_ps, prob.thresh = 0.5, log2.thresh = 1,
include.cent = F, degenerate.pwms = F, .degenerate.groups = c("DE",
"KR", "ILMV"))
|
obj |
MIMP kinase object containing PWM, auc, GMM parameters, family name, etc. |
mut_ps |
psnvs data frame containing wt and mt sequences computed from pSNVs function |
prob.thresh |
Probability threshold of gains and losses. This value should be between 0.5 and 1. |
log2.thresh |
Threshold for the absolute value of log ratio between wild type and mutant scores. Anything less than this value is discarded (default: 1). |
include.cent |
If TRUE, gains and losses caused by mutation in the central STY residue are kept |
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