inst/dataprep/Data_Join.R

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

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

# names of current objects
currObjVec = ls()

# Data Join ---------------------------------------------------------------

### EDIT TABLES FOR JOINING

# Goal: Ensure tables all have the same columns before joining, and
# that the people who need to be excluded from the BCG tables are excluded.

### lOrigMainTbl

joinOrigMainTbl = lOrigMainTbl %>% mutate( ptid = as.character( ptid ) )

joinOrigMainITbl = lOrigMainITbl %>% mutate( ptid = as.character( ptid ) )

### h1Tbl

joinH1Tbl = h1Tbl %>%
  rename( frequency = freq ) %>%
  select( -c( ag85b, esat6 ) ) %>%
  mutate( prid = "7", vaccine = "5" )

joinH1ITbl = h1ITbl %>%
  filter( stim != "freq" ) %>%
  rename( frequency = resp ) %>%
  mutate( prid = "7", vaccine = "5" )

### l4Tbl

join4Tbl = l4Tbl %>%
  mutate( vaccine = "7", prid = "8", infxn = "1" ) %>%
  filter( group == 'IBO') %>%
  select( -group )

join4ITbl = l4ITbl %>%
  mutate( vaccine = "7", prid = "8", infxn = "1" ) %>%
  filter( group == 'IBO') %>%
  select( -group )

### l8Tbl

join8Tbl = l8Tbl %>%
  mutate( vaccine = "7", prid = "8", infxn = "1" ) %>%
  filter( group == 'IBO') %>%
  select( -group )

join8ITbl = l8ITbl %>%
  mutate( vaccine = "7", prid = "8", infxn = "1" ) %>%
  filter( group == 'IBO') %>%
  select( -group )

### h564Tbl

join564Tbl = h564Tbl %>%
  filter( dose == 5 ) %>%
  filter( group == 1 | group == 3 ) %>%
  select( -c( group, dose, doseCount ) ) %>%
  mutate( vaccine = "2", prid = "2" ) %>%
  gather( key = cytCombo, value = frequency, CD4Gp2pTp17p:CD4Gn2nTn17p )


join564ITbl = h564ITbl %>%
  filter( dose == 5 ) %>%
  filter( group == 1 | group == 3 ) %>%
  select( -c( group, dose, doseCount ) ) %>%
  mutate( vaccine = "2", prid = "2" ) %>%
  gather( key = cytCombo, value = frequency, CD4Gp2pTp17p:CD4Gn2nTn17p )

### h568Tbl

join568Tbl = h568Tbl %>%
  filter( dose == 5 ) %>%
  filter( group == 1 | group == 3 ) %>%
  select( -c( group, dose, doseCount ) ) %>%
  mutate( vaccine = "2", prid = "2" ) %>%
  gather( key = cytCombo, value = frequency, CD8Gp2pTp17p:CD8Gn2nTn17p )

join568ITbl = h568ITbl %>%
  filter( dose == 5 ) %>%
  filter( group == 1 | group == 3 ) %>%
  select( -c( group, dose, doseCount ) ) %>%
  mutate( vaccine = "2", prid = "2" ) %>%
  gather( key = cytCombo, value = frequency, CD8Gp2pTp17p:CD8Gn2nTn17p )

# idriTbl

joinIdriTbl = idriTbl %>%
  select( -group ) %>%
  mutate( vaccine = "6", prid = "9",
          timePoint = as.numeric( timePoint ) )%>%
  gather( key = cytCombo, value = frequency, CD8Gp2pTp17p:CD4Gn2nTn17p )

joinIdriITbl = idriITbl %>%
  select( -group ) %>%
  mutate( vaccine = "6", prid = "9",
          timePoint = as.numeric( timePoint ) )%>%
  gather( key = cytCombo, value = frequency, CD8Gp2pTp17p:CD4Gn2nTn17p )

# aerasTbl

joinAerasTbl = aerasTbl %>%
  mutate( prid = '1',
          timePoint = as.character( timePoint ) ) %>%
  gather( key = cytCombo, value = frequency, Gn2nTn17p:Gp2pTp17p ) %>%
  mutate( cytCombo = str_c( "CD", cd, cytCombo ) ) %>%
  select( -cd )

joinAerasITbl = aerasITbl %>%
  mutate( prid = '1',
          timePoint = as.character( timePoint ) ) %>%
  gather( key = cytCombo, value = frequency, Gn2nTn17p:Gp2pTp17p ) %>%
  mutate( cytCombo = str_c( "CD", cd, cytCombo ) ) %>%
  select( -cd )

### JOIN TABLES

firstJoinTbl = bind_rows( joinOrigMainTbl, join4Tbl, join8Tbl, join564Tbl, join568Tbl, joinIdriTbl, joinH1Tbl ) %>%
  rbind( joinAerasTbl ) %>%
  filter( str_sub( cytCombo, start = 4 ) != "Gn2nTn17n" ) %>%
  arrange( vaccine, infxn, prid, ptid, timePoint ) %>%
  mutate( frequency = sapply( frequency, max, 0 ) )

firstJoinITbl = bind_rows( joinOrigMainITbl, join4ITbl, join8ITbl, join564ITbl, join568ITbl, joinIdriITbl, joinH1ITbl  ) %>%
  rbind( joinAerasITbl ) %>%
  filter( str_sub( cytCombo, start = 4 ) != "Gn2nTn17n" ) %>%
  arrange( vaccine, infxn, prid, ptid, timePoint ) %>%
  mutate( frequency = sapply( frequency, max, 0 ) )

# Join tables -------------------------------------------------------------

join17IncTbl = firstJoinTbl %>%
  filter( cytCombo != 'CD4Gn2nTn17n' & cytCombo != 'CD8Gn2nTn17n' ) %>%
  arrange( vaccine, prid, infxn, ptid, cytCombo, timePoint  ) %>%
  mutate( ptid = as.character( ptid ) ) %>%
  select( ptid:infxn, timePoint, cytCombo, frequency ) %>%
  ungroup() %>%
  mutate( timePoint = as.numeric( timePoint ) ) %>%
  arrange( vaccine, prid, infxn, ptid, cytCombo, timePoint ) %>%
  rename( resp = frequency ) %>%
  mutate( resp = pmax( resp, 0 ) )

join17IncITbl =  firstJoinITbl %>%
  filter( cytCombo != 'CD4Gn2nTn17n' & cytCombo != 'CD8Gn2nTn17n' ) %>%
  arrange( vaccine, prid, infxn, ptid, cytCombo, stim, timePoint  ) %>%
  mutate( ptid = as.character( ptid ) ) %>%
  select( ptid:infxn, stim, timePoint, cytCombo, frequency ) %>%
  ungroup() %>%
  mutate( timePoint = as.numeric( timePoint ) ) %>%
  arrange( vaccine, prid, infxn, ptid, stim, cytCombo, timePoint ) %>%
  rename( resp = frequency ) %>%
  mutate( resp = pmax( resp, 0 ) )

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

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