regionAnalysis: Summary of HMM Regions

In USCDTG/tLOH: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Summary of HMM Regions

Description

Generates summary metrics for HMM regions

Usage

regionAnalysis(originalDF,dataframeList)

Arguments

originalDF	Original imported dataframe from tLOHCalcUpdated
dataframeList	List of HMM state determination dataframes from the run_HMM series of functions

Value

Output is a dataframe containing region metrics and data for each HMM segment

Author(s)

Michelle Webb

Examples

data('humanGBMsampleAC')
data('initialStartProbabilities')
df <- tLOHCalcUpdate(humanGBMsampleAC,1.25,1.25,500,500,4)
dataframeList <- prepareHMMdataframes(df)
trProbs <- cbind(c(0.8999,0.1001),c(0.1001,0.8999))
dataframeList2 <- runHMM_1(dataframeList, initialStartProbabilities, trProbs)
dataframeList3 <- runHMM_2(dataframeList2)
output <- runHMM_3(dataframeList3)
final <- regionAnalysis(dataframeList,output)

USCDTG/tLOH documentation built on Oct. 23, 2022, 8:05 p.m.