perc.permutation

results

permutations

<p>Get percentile ranks across permutations</p>

internal

A tool for inferring kinase activity changes from
phosphoproteomics data. 'pKSEA' uses kinase-substrate
prediction scores to weight observed changes in
phosphopeptide abundance to calculate a phosphopeptide-level
contribution score, then sums up these contribution scores by
kinase to obtain a phosphoproteome-level kinase activity
change score (KAC score). 'pKSEA' then assesses the
significance of changes in predicted substrate abundances for
each kinase using permutation testing. This results in a
permutation score (pKSEA significance score) reflecting the
likelihood of a similarly high or low KAC from random chance,
which can then be interpreted in an analogous manner to an
empirically calculated p-value. 'pKSEA' contains default
databases of kinase-substrate predictions from 'NetworKIN'
(NetworKINPred_db) <http://networkin.info>
Horn, et. al (2014) <doi:10.1038/nmeth.2968>
and of known kinase-substrate links from 'PhosphoSitePlus'
(KSEAdb) <https://www.phosphosite.org/>
Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.

perc.permutation: Get percentile ranks across permutations

Description

Usage

Arguments