permtest {pKSEA} | R Documentation |
Perform permutation test
Description
Returns a table that has permuted the relationship between phosphopeptides and summary statistics (ie. fold change, t-score)
Usage
permtest(matched_data, perms = 1000, seed = 1)
Arguments
matched_data |
Input with calculated contributions |
perms |
Number of permutations to run, default = 1000 |
Value
dataframe with kinases as rows, each column as KAC scores calculated from one permutation
Examples
#Read in example summary statistics dataset from csv
summarydata_ex <- read.csv(system.file("extdata", "example_data1.csv", package="pKSEA"))
#Get matched data using predictions from NetworKIN
matched_data_ex <- get_matched_data(summarydata_ex, NetworKINPred_db)
#Calculate contributions
calc_ex <- calc_contribution(matched_data_ex)
#Perform 5 permutations
perm_ex <- permtest(calc_ex, perms= 5, seed= 123)
[Package pKSEA version 0.0.1 Index]