inst/dataprep/H1.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/h1.xlsx" )
h1Tbl = as_tibble( read.xlsx( fileLoc, sheet = 'Sheet 1') )

# table with info of which IDs are in group 1
fileLoc = paste0( pkgPath, "/extdata/h1-group_info.xlsx" )
fTbl = as_tibble( read.xlsx( fileLoc ) )

# francesca's data
groupOnePtidVec = fTbl %>%
  filter( Group == 1 ) %>%
  `[[`( 'SubjectID' ) %>%
  unique()

# Data Prep ---------------------------------------------------------------

# rename and select columns
h1Tbl %<>%
  rename( ptid = SAMPLE.ID, stim = TUBE.NAME, timePoint = Timepoint, group = Group ) %>%
  select( -c( Sample, `$FIL` ) )

# h1Tbl$group %>% unique() # 1 2, so only two groups for some reason.

# further editing
h1Tbl %<>%
  mutate( stim = str_to_lower( stim ),
          timePoint = as.character( timePoint ) %>% str_trim(),
          ptid = as.character( ptid ) ) %>%
  filter( ptid %in% groupOnePtidVec ) %>%
  rename( infxn = group ) %>%
  separate( col = timePoint, into = c( "Useless", "Number" ) ) %>%
  mutate( timePoint = as.numeric( Number ),
          infxn = sapply( infxn, function( x ) ifelse( x == 2, '1', '0' ) ) ) %>%
  select( -c( Useless, Number ) ) %>%
  select( ptid, infxn, timePoint, stim, everything() ) %>%
  arrange( infxn, ptid, timePoint, stim )

# h1Tbl$stim %>% unique() # ""Ag85B" "ESAT6" "PHA"   "UNS". make lower case
# h1Tbl$ptid %>% unique() # all numbers. Correct
# h1Tbl$timePoint %>% unique()  #  0  14  56  70 224, post transform. Correct.
# h1Tbl %>% group_by( ptid ) %>% slice( 1 ) %>% ungroup() %>% group_by( infxn ) %>% summarise( count = n() ) # 1 - 34. 2 - 24. So group is infxn status.

# edit cytCombo names

origCytVec = dimnames( h1Tbl )[[2]][5:ncol( h1Tbl )]

altCytVec = sapply( origCytVec, function( x ) str_c( str_sub( x, 1, 3 ), editNonANStr( x, 6, 7 ) , editNonANStr( x, 10, 11), editNonANStr( x, 8, 9 ), editNonANStr( x, 12, 14 ), collapse ="" ) )

dimnames( h1Tbl )[[2]][5:ncol( h1Tbl )] = altCytVec

# check stims

invisible( h1Tbl %>%
             group_by( ptid, timePoint ) %>%
             summarise( totStim = str_c( stim, collapse = "" ) ) %>%
             ungroup() %>%
             group_by( totStim ) %>%
             summarise( count = n() ) ) # ag85besat6phauns   281. Everyone had all.

# sum over stims, and make long
h1Tbl %<>%
  gather( key = cytCombo, value = freq, CD4Gp2pTp17p:CD8Gn2nTn17n ) %>%
  arrange( infxn, ptid, cytCombo, timePoint, stim ) %>%
  group_by( infxn, ptid, timePoint, cytCombo ) %>%
  summarise( ag85b = freq[1] - freq[4], esat6 = freq[2] - freq[4], freq = freq[1] + freq[2] - 2 * freq[4]  ) %>%
  ungroup() %>%
  arrange( infxn, ptid, cytCombo, timePoint )

h1ITbl = h1Tbl %>%
  gather( key = stim, value = resp, ag85b:freq )

# remove all cytoCombo negatives
h1ITbl %<>% filter( cytCombo != 'CD4Gn2nTn17n' & cytCombo != 'CD8Gn2nTn17n'  & stim != 'freq')

h1Tbl %<>% filter( cytCombo != 'CD4Gn2nTn17n' & cytCombo != 'CD8Gn2nTn17n' )

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

# h1ITbl
testVal1 = h1ITbl %>%
  filter( ptid == 'h1_2' & timePoint == 0 & stim == "esat6" & cytCombo == "CD4Gp2nTn17n" ) %>%
  extract2("resp")
if( testVal1 != ( 0.001113883 - 0.0005162169 ) ) stop( "h1ITbl error")
testVal2 = h1ITbl %>%
  filter( ptid == 'h1_221' & timePoint == 224 & stim == "ag85b" & cytCombo == "CD8Gp2nTp17n" ) %>%
  extract2("resp")
if( testVal2 != ( 0.001595456 - 0.003927473 ) ) stop( "h1ITbl error" )

# h1ITbl
testVal1 = h1Tbl %>%
  filter( ptid == 'h1_81' & timePoint == 14 & cytCombo == "CD4Gn2nTp17n" ) %>%
  extract2("freq")
if( testVal1 != ( 0.00165674 + 0.002524785 - 2 * 0.001658691 ) ) stop( "h1Tbl error")

testVal2 = h1Tbl %>%
  filter( ptid == 'h1_81' & timePoint == 14 & cytCombo == "CD4Gp2pTn17n" ) %>%
  extract2("freq")
if( testVal2 != ( 0.00414185 +  0.002524785 - 2 * 0 ) ) stop( "h1Tbl error")

# Clear workspace ---------------------------------------------------------

# remove all objects but initial objects (currObjVec) and processed data tibble (l4Tbl)
rm( list = setdiff( ls(), c( currObjVec, "h1Tbl", "h1ITbl" ) ) )