inst/dataprep/Main.R

In MiguelRodo/VaccCompData: Data package for novel TBV vaccine comparison paper

# Loading -----------------------------------------------------------------

# names of current objects
currObjVec = ls()

# find library containing raw data
pkgPath = system.file( package = "VaccCompData" )

# libraries
source( file = paste0( pkgPath, "/dataprep/libraries.R") )

#read in data
fileLoc = paste0( pkgPath, "/extdata/main.xlsx" )
tbData = as_tibble( read.xlsx( fileLoc, sheet = 'Sheet 1') )

# Data Preparation ------------------------------------------------

# column editing

tbData %<>%
  rename( 'ptid' = PatientID, 'prid' = Protocol.ID, vaccine = Vaccine, infxn = Infxn,
          timePoint = TimePoint ) %>%
  select(-c(TubeName, UniqueID) ) %>%
  mutate( vaccine = convVaccNameToInteger( vaccine ),
          prid = convProtNameToInteger( prid ),
          infxn = str_trim( infxn ),
          infxn = ifelse( infxn == 'positive', 1, 0 ),
          infxn = as.character( infxn ) ) %>%
  arrange( vaccine, prid, infxn, ptid, timePoint )

# select only multiple cytokines

tbData %<>%
  gather( key = cytCombo, value = frequency, `CD4posGpos2pos17posTpos`:`TotCD8posTpos` ) %>%
  filter( str_length( cytCombo ) > 20  ) %>%
  spread( key = cytCombo, value = frequency ) %>%
  arrange( vaccine, prid, infxn, ptid, timePoint )

# rename booleans

tbData %<>% rename( CD8posGNeg2pos17posTNeg = CDpos8GNeg2pos17posTNeg  )

origCytVec = dimnames( tbData )[[2]][6:35]

altCytVec = sapply( origCytVec, function( x ) str_c( str_sub( x, 1, 3 ), editStr( x, 7, 8 ) , editStr( x, 11, 12 ), editStr( x, 20, 21 ), editStr( x, 15, 17 ), collapse ="" ) )

dimnames( tbData )[[ 2 ]][6:35] = altCytVec

# make all Aeras402 uninfected
tbData[ which( tbData$vaccine == 1 ),  'infxn' ] = 0

# make long
lOrigMainTbl = tbData %>%
  gather( key = cytCombo, value = frequency, CD4Gn2nTp17n:CD8Gn2pTn17p ) %>%
  filter( cytCombo != 'CD4Gn2nTn17n' & cytCombo != 'CD8n2nTn17n' )

# add in stim column
lOrigMainITbl = lOrigMainTbl %>%
  mutate( stim = nameStim( vaccine ) )

# Testing -----------------------------------------------------------------

# lOrigMainITbl
testVal1 = lOrigMainITbl %>%
  filter( ptid == 'main_1' & vaccine == 3 & timePoint == 0 & stim == "m72ppl" & cytCombo == "CD4Gn2pTp17n" ) %>%
  extract2("frequency")
if( testVal1 != 0.009 ) stop( "lOrigMainITbl error")
testVal2 = lOrigMainITbl %>%
  filter( ptid == 'main_91' & vaccine == 4 & infxn == 0 & timePoint == 7 & stim == "ag85a" & cytCombo == "CD4Gp2pTp17p" ) %>%
  extract2("frequency")
if( testVal2 != 0.041 ) stop( "lOrigMainITbl error" )
testVal3 = lOrigMainITbl %>%
  filter( ptid == 'main_102' & vaccine == 4 & infxn == 1 & timePoint == 364 & stim == "ag85a" & cytCombo == "CD8Gn2nTn17p" ) %>%
  extract2("frequency")
if( testVal3 != 0.002 ) stop( "lOrigMainITbl error" )

# lOrigMainTbl
testVal1 = lOrigMainTbl %>%
  filter( ptid == 'main_1' & vaccine == 3 & timePoint == 0 & cytCombo == "CD4Gn2pTp17n" ) %>%
  extract2("frequency")
if( testVal1 != 0.009 ) stop( "lOrigMainTbl error")
testVal2 = lOrigMainTbl %>%
  filter( ptid == 'main_91' & vaccine == 4 & infxn == 0 & timePoint == 7 & cytCombo == "CD4Gp2pTp17p" ) %>%
  extract2("frequency")
if( testVal2 != 0.041 ) stop( "lOrigMainTbl error" )
testVal3 = lOrigMainTbl %>%
  filter( ptid == 'main_102' & vaccine == 4 & infxn == 1 & timePoint == 364 & cytCombo == "CD8Gn2nTn17p" ) %>%
  extract2("frequency")
if( testVal3 != 0.002 ) stop( "lOrigMainTbl error" )

# Clear Workspace ---------------------------------------------------------

# remove all objects but initial objects (currObjVec) and processed data tibble (l8Tbl)
rm( list = setdiff( ls(), c( currObjVec, "lOrigMainTbl", "lOrigMainITbl" ) ) )