inst/dataprep/IL_17-Calc_And_Removal.R

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

# Set-up ------------------------------------------------------------------

# names of current objects
currObjVec = ls()

# Megapool data preparation --------------------------------------------------------

# megTbl
# uniqueOrigPTIDVec = unique( megTbl$ptid )
# startPTID = max( as.numeric( join17ExcTbl$ptid ) ) + 1
# endPTID = startPTID + calcLU( uniqueOrigPTIDVec )
# repPTIDLabVec = setNames( startPTID:endPTID %>% as.character(), uniqueOrigPTIDVec )
joinMegTbl1 = megTbl %>%
  # mutate( ptid = repPTIDLabVec[ptid] ) %>%
  select( ptid, infxn, timePoint, everything() ) %>%
  mutate( vaccine = "8", prid = "10", timePoint = as.numeric( timePoint ) ) %>%
  gather( key = cytCombo, value = resp, CD4Gn2nTp:CD8Gp2pTp )

joinMegITbl1 = megITbl %>%
  # mutate( ptid = repPTIDLabVec[ptid] ) %>%
  select( ptid, infxn, timePoint, everything() ) %>%
  mutate( vaccine = "8", prid = "10", timePoint = as.numeric( timePoint ) ) %>%
  gather( key = cytCombo, value = resp, CD4Gn2nTp:CD8Gp2pTp )

# IL-17 Single -----------------------------------------------------------------

single17Tbl = join17IncTbl %>%
  filter( str_sub( cytCombo, start = -1L ) == 'p' ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) ) %>%
  group_by( vaccine, infxn, prid, ptid, cd,  timePoint ) %>%
  summarise( resp = sum( resp ) ) %>%
  ungroup()

single17ITbl = join17IncITbl %>%
  filter( str_sub( cytCombo, start = -1L ) == 'p' ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) ) %>%
  group_by( vaccine, infxn, prid, ptid, cd,  timePoint, stim ) %>%
  summarise( resp = sum( resp ) ) %>%
  ungroup()

# Sum over IL-17 ----------------------------------------------------------

# sum over il17
join17ExcTbl = join17IncTbl %>%
  mutate( shortCytCombo = str_sub( cytCombo, end = -4 ) ) %>%
  group_by( vaccine, prid, infxn, ptid, timePoint, shortCytCombo ) %>%
  summarise( resp = sum( resp ) ) %>%
  ungroup() %>%
  rename( cytCombo = shortCytCombo  ) %>%
  filter( str_sub( cytCombo, 4 ) != "Gn2nTn" ) %>%
  filter( !( ptid == 28 & str_sub( cytCombo, 3, 3 ) == 4 & timePoint == 70 ) ) %>%
  bind_rows( joinMegTbl1 )

# sum over il17

join17ExcITbl = join17IncITbl %>%
  mutate( shortCytCombo = str_sub( cytCombo, end = -4 ) ) %>%
  group_by( vaccine, prid, infxn, ptid, stim, timePoint, shortCytCombo ) %>%
  summarise( resp = sum( resp ) ) %>%
  ungroup() %>%
  rename( cytCombo = shortCytCombo  ) %>%
  filter( str_sub( cytCombo, 4 ) != "Gn2nTn" ) %>%
  filter( !( ptid == 28 & str_sub( cytCombo, 3, 3 ) == 4 & timePoint == 70 ) ) %>%
  bind_rows( joinMegITbl1 )

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

# remove all objects but initial objects (currObjVec) and processed data tibble (l8Tbl)
rm( list = setdiff( ls(), c( currObjVec, "join17IncTbl", "single17Tbl", "join17ExcTbl", "join17IncITbl",
                             "single17ITbl", "join17ExcITbl", "joinMegTbl1", "joinMegITbl1" ) ) )