inst/dataprep/H56-CD8.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/h56.xlsx" )
cd8Tbl = as_tibble( read.xlsx( fileLoc, sheet = 'CD8 Freq') )

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

#UNIQUE VALUES

#unique values in id info
unique(cd8Tbl$Stimulation) #"Ag85B"  "ESAT6"  "PHA"    "Rv2660" "UNS". Make lower case.
unique(cd8Tbl$Study.Day) #0  14  56  70 292 112 126. Correct
unique(cd8Tbl$LTBI) # "neg" "pos". Correct, but convert to 0 1
unique(cd8Tbl$Group) # 1 2 3 4. Correct
unique(cd8Tbl$`Vaccine/Placebo`) # "vaccine" "placebo". Correct, but convert to 0 1
unique(cd8Tbl$Dose) # 15 5 50 0 . Correct
unique(cd8Tbl$`Regimen.(#injections)`) # 2 1 3. Corrrect.

# renaming columns and converting to correct type
cd8Tbl %<>% mutate( Stimulation = str_to_lower(Stimulation) ) %>%
  rename( group = Group, inf = LTBI, ptid = PTID, stim = Stimulation, timePoint = Study.Day, treatType = `Vaccine/Placebo`, dose = Dose ) %>%
  mutate( group = as.character( group ), inf = as.character( inf ), dose = as.character( dose ), timePoint = as.character( timePoint ) ) %>%
  rename( infxn = inf )

# correct day 292 and PTID ID_03017
#cd8Tbl[ cd8Tbl$ptid == 'ID_03017', "treatType" ] = 'vaccine'
#cd8Tbl[ cd8Tbl$ptid == 'ID_03017', "dose" ] = "5"
cd8Tbl[ cd8Tbl$ptid == 'h56_75', "treatType" ] = 'vaccine'
cd8Tbl[ cd8Tbl$ptid == 'h56_75', "dose" ] = "5"

# dimension names
dimnames(cd8Tbl)[[2]][8] = 'doseCount'

# change doseCount variable type
cd8Tbl %<>% mutate( doseCount = as.character( doseCount ) )

# editing entries
cd8Tbl %<>%
  mutate( infxn = sapply( infxn, function(x) ifelse( x == 'neg', '0', '1' ) ),
          ptid = str_to_lower( ptid ),
          stim = str_to_lower( stim ),
          treatType = sapply( treatType, function(x) ifelse( x == 'vaccine', '1', '0' ) ) )

### BOOLEAN COLUMN NAMES
cd8Tbl2 = cd8Tbl
# remove useless columns
cd8Tbl %<>% select( -c( `CD8+`, `g-T-2-17-`, `CD8+g+`, `CD8+T+`, `CD8+2+`, `CD8+17+` ))

# get actual names
cytNameVec = str_to_upper( tbl_vars(cd8Tbl)[9:23] )

# get replacement names
for (i in 1:length(cytNameVec)){ #loop over names
  currCyt = cytNameVec[i]
  #check if we have a positive in a given location
  #if so, add a p onto a string. If not, add an n
  locVec = c(2,4,6,9)
  signVec = str_sub(currCyt, locVec,locVec)
  for (j in 1:length(signVec)){
    if (signVec[j] == '+'){
      str_sub(currCyt, locVec[j], locVec[j]) = 'p'
    } else if (signVec[j] == '-'){
      str_sub(currCyt, locVec[j], locVec[j]) = 'n'
    }
  }
  cytNameVec[i] = currCyt
}

# replace names

origCytNameVec = tbl_vars(cd8Tbl)[9:23]
colNameCodeDF = data_frame(x = str_c("cd8Tbl %>% rename( cd8", cytNameVec, " = `", origCytNameVec, "`)"))

cd8Tbl = eval(parse(text = colNameCodeDF[1,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[2,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[3,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[4,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[5,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[6,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[7,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[8,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[9,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[10,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[11,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[12,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[13,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[14,1]))
cd8Tbl = eval(parse(text = colNameCodeDF[15,1]))

### remove placebo
cd8Tbl %<>%
  filter( treatType == 1 ) %>%
  select( -treatType )

### RE-ORDER

cd8Tbl = changeCytOrder( dataTibble = cd8Tbl, firstCytColIndex = 8,
                          firstCytNameLoc = 4, signLocVec = c( 5, 7, 9, 12 ),
                          orderLocVec = c( 1, 3, 2, 4 ), cdPresent = TRUE )

# Data Checking -----------------------------------------------------------

# stim
# four stims
cd8Tbl %>%
  group_by( infxn, group, ptid, timePoint ) %>%
  summarise( stimCount = n() ) %>%
  filter( stimCount != 5 )

viewTbl = cd8Tbl %>%
  filter( ptid == 'id_03008' | ptid == 'id_03019' ) %>%
  filter( timePoint == 14 )
#print( viewTbl, n =  10^19 ) # both are missing unstim.

cd8Tbl %>%
  arrange( infxn, group, ptid, timePoint, stim ) %>%
  group_by( infxn, group, ptid, timePoint ) %>%
  summarise( stimVec = str_c(stim, sep = "", collapse = "" ) ) %>%
  filter( stimVec != "ag85besat6pharv2660uns") # same as above, so everyone else has all the right stims for each day.

# remove rows
cd8Tbl %<>%
  filter( !( ptid == 'h56_86' & timePoint == '14' ) ) %>%
  filter( !( ptid == 'h56_90' & timePoint == '14' ) )


# Subtraction -------------------------------------------------------------

########################
### SUB UNS FROM BCG ###
########################

# check
cd8Tbl %>%
  arrange( infxn, group, ptid, timePoint, stim ) %>%
  group_by( infxn, group, ptid, timePoint ) %>%
  summarise( stimVec = str_c(stim, sep = "", collapse = "" ) ) %>%
  filter( stimVec != "ag85besat6pharv2660uns") # none with missing values

# save non-summed over table
cd8ITbl = cd8Tbl %>%
  group_by( group, infxn, ptid, dose, doseCount, timePoint ) %>%
  mutate_if( is.numeric, function(x) x - x[5] ) %>%
  ungroup() %>%
  filter( stim %in% c( "ag85b", "esat6", "rv2660" ) )

# summation
cd8Tbl %<>%
  group_by( group, infxn, ptid, dose, doseCount, timePoint ) %>%
  summarise_if( is.numeric, function(x) sum( x[ c( 1, 2, 4 ) ] ) - 3 * x[ 5 ] ) %>%
  ungroup()

# Data Editing ------------------------------------------------------------

h568ITbl = cd8ITbl %>%
  mutate( timePoint = as.numeric( timePoint ) )

h568Tbl = cd8Tbl %>%
  mutate( timePoint = as.numeric( timePoint ) )

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

# h564ITbl
testRow1 = h568ITbl %>% filter( ptid == 'h56_33' & timePoint == 0 & stim == "esat6" )
if( testRow1$CD8Gp2nTn17n != ( 0.003297 - 0.000829 ) ) stop( "h568ITbl error" )
testRow2 = h568ITbl %>% filter( ptid == 'h56_97' & timePoint == 126 & stim == "ag85b" )
if( testRow2$CD8Gp2nTn17p != ( 0.001711 - 0.003881 ) ) stop( "h568ITbl error" )
# h564Tbl
testRow1 = h568Tbl %>% filter( ptid == 'h56_96' & timePoint == 56 )
if( testRow1$CD8Gn2pTn17n != ( 0.000539 + 0.002565 + 0.001957 - 3 * 0.000542 ) ) stop( "h568Tbl error")

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


# remove all objects but initial objects (currObjVec) and processed data tibble (h564Tbl)
rm( list = setdiff( ls(), c( currObjVec, "h568Tbl", "h568ITbl" ) ) )