summarizeRegions2: Step 2 of region summary

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

Step 2 of region summary

Description

Function used by regionFinalize to identify segment start and end positions

Usage

summarizeRegions2(finalTable)

Arguments

finalTable

A dataframe containing metrics from the Bayes Factor and HMM analysis

Value

Output is a dataframe

Author(s)

Michelle Webb

Examples

## Not run: 
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)
intermediate <- regionAnalysis(dataframeList,output)
finalList1 <- purrr::map(intermediate, 
~dplyr::mutate(.x, state = as.character(state)))
sampleValues <- as.data.frame(purrr::reduce(finalList1,full_join))
sampleData <- summarizeRegions1(finalList1)
sampleData$lengthOfInterval <- sampleData$intervalEnd - sampleData$intervalStart
sampleDF <- summarizeRegions2(sampleValues)
## End(Not run)

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