permtest function

Perform permutation test

Returns a table that has permuted the relationship between phosphopeptides and summary statistics (ie. fold change, t-score)

permtest(matched_data, perms = 1000, seed = 1)

Arguments

• matched_data: Input with calculated contributions
• perms: Number of permutations to run, default = 1000

Returns

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)