Description Usage Arguments Value Examples
View source: R/internal_functions.R
Returns a table that has permuted the relationship between phosphopeptides and summary statistics (ie. fold change, t-score)
1 | permtest(matched_data, perms = 1000, seed = 1)
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matched_data |
Input with calculated contributions |
perms |
Number of permutations to run, default = 1000 |
dataframe with kinases as rows, each column as KAC scores calculated from one permutation
1 2 3 4 5 6 7 8 9 10 11 | #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)
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