getSeqPatterns: Get sequential patterns

In novasmedley/gbmSpm: Find predictive sequential patterns for clinical glioblastoma patients

Description

Get sequential patterns

Usage

getSeqPatterns(event, transFilename, createT, support, maxgap, maxlen, maxsize)

Arguments

event	dataframe of events, where rows are single events, and least the following columns: iois patient id eventID event id, see resetEventIDsToDays eventName unique event name, see createEventNames
transFilename	asdf
createT	logical, create or load previously created transactions
support	see slot in SPparameter-class
maxgap	see slot in SPparameter-class
maxlen	see slot in SPparameter-class
maxsize	see slot in SPparameter-class

Value

a named list containing:

• freqseq, the output from arulesSequences::cspade

• data, the input data

See Also

createTransactions

Examples

data("fake_data")
outputDir <- '~/test'

# save tumor location and laterility strings before event cleaning
fake_tumorInfo <- fake_data$events 
fake_demo <- fake_data$demo

# clean data
fake_data$events <- cleanData(fake_data$events, tType = 'rate')
cat('...',nrow(fake_data$events), " events left for SPM after cleaning", '\n')

# collect patient info for each event
fake_data <- merge(fake_data$events, fake_data$person, by='iois', all.x=T) 

# prep for each event, since age does change
# get survival labels, these also change
fake_data <- prepDemographics(fake_data, fake_demo) 
fake_data <- prepSurvivalLabels(fake_data) 

# get first tumor location
fake_data <- getTumorLocation(fake_data, fake_tumorInfo) 

# spm
pSPM <- getSeqPatterns(event = fake_data,
                       transFilename = file.path(outputDir, 'example_transactions.txt'),
                       createT = T,
                       support = 0.4,
                       maxgap = 60,
                       maxlen = 2,
                       maxsize = 2)

novasmedley/gbmSpm documentation built on May 17, 2019, 10:39 a.m.