inst/dataprep/AERAS402.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/aeras402.xlsx" )
aerasTbl = as_tibble( read.xlsx( fileLoc ) )

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

#UNIQUE VALUES

#unique values in id info
unique(aerasTbl$PatientID) # "051-25" "139-23" "226-21" "234-28" "250-24" "265-27" "292-30" "355-40" "360-36"
unique(aerasTbl$TubeName) # "Ag85"   "BCG"    "TB10.4"
unique(aerasTbl$TimePoint) #  0   7  28  84 182

# edit columns
aerasTbl %<>%
  rename( ptid = PatientID,
    stim = TubeName,
    timePoint = TimePoint ) %>%
  mutate_at( vars( `CD4+2+17+G+T+`:`CD8+2-17-G-T+` ), as.numeric ) %>%
  mutate( stim = str_to_lower( stim ),
    infxn = "0",
    vaccine = "1" ) %>%
  select( vaccine, ptid, infxn, stim, timePoint, everything() ) %>%
  arrange( vaccine, ptid, infxn, stim, timePoint ) %>%
  mutate( timePoint = as.character( timePoint ) )

aerasTbl %<>%
  filter( stim != 'bcg' ) %>%
  mutate( stim = Vectorize(ifelse)( stim == "tb10.4", "tb104", stim ) ) %>%
  rename_if( is.numeric, function( x ) str_rep_pos_neg( x ) ) %>%
  rename_if( is.numeric, function(x) str_to_upper_sel( x, c( "p", "n" ) ) ) %>%
  gather( key = cytCombo, value = resp, CD4p2p17pGpTp:CD8p2n17nGnTp ) %>%
  mutate( cd = str_sub( cytCombo, 3, 3 ),
    cytCombo = str_sub( cytCombo, 5 ) ) %>%
  spread( key = cytCombo, value = resp ) %>%
  rename_if( is.numeric, function(x) str_chunk_reorder( x, c( "p", "n" ), c( 2, 4, 1, 3 ) ) ) %>%
  gather( key = cytCombo, value = resp, Gn2nTp17n:Gp2pTp17p ) %>%
  mutate( timePoint = as.numeric( timePoint ) ) %>%
  arrange( vaccine, ptid, infxn, cd, timePoint, cytCombo, stim ) %>%
  # mutate( ptid = str_c( "xyz", ptid ) ) %>%
  spread( key = cytCombo, value = resp ) %>%
  arrange( vaccine, ptid, infxn, cd, timePoint, stim ) %>%
  mutate( timePoint = as.character( timePoint ) )

# stim

# number of stims
aerasTbl %>%
  group_by( infxn, ptid, timePoint, cd ) %>%
  summarise( stimCount = n() ) %>%
  filter( stimCount != 3 ) # all have three stims per time point and cytCombo

# number of unique stims
aerasTbl %>%
  group_by( infxn, ptid, timePoint, cd ) %>%
  summarise( uniqueStimCount = n_distinct( stim ) ) %>%
  filter( uniqueStimCount != 3 ) # all have five unique stims.

# all in same order
aerasTbl %>%
  group_by( vaccine, infxn, ptid, timePoint, cd ) %>%
  summarise( stimStr = str_c( stim, collapse = "" ) ) %>%
  extract2( "stimStr" ) %>%
  calcLU()
# Subtraction -------------------------------------------------------------

aerasITbl = aerasTbl

# summation

aerasTbl %<>%
  group_by( vaccine, ptid, infxn, timePoint, cd ) %>%
  summarise_if( is.numeric, function(x) sum(x) ) %>%
  ungroup()

# Tests -------------------------------------------------------------------

# aerasITbl
testRow1 = aerasITbl %>% filter( ptid == 'aeras_1' & timePoint == 0 & stim == "ag85" & cd == "8" )
if( testRow1$Gn2pTn17n != 0.024 ) stop( "aerasITbl error")
testRow2 = aerasITbl %>% filter( ptid == 'aeras_9' & timePoint == 182 & stim == "tb104" & cd == "4" )
if( testRow2$Gn2pTp17n != 0.00141 ) stop( "aerasITbl error")
testRow3 = aerasITbl %>% filter( ptid == 'aeras_9' & timePoint == 7 & stim == "ag85" & cd == "4" )
if( testRow3$Gp2nTp17p != 0.00185) stop( "aerasITbl error")
testRow4 = aerasITbl %>% filter( ptid == 'aeras_8' & timePoint == 0 & stim == "tb104" & cd == "4" )
if( testRow4$Gn2pTp17n != 0.00404) stop( "aerasITbl error")

# aerasTbl
testRow1 = aerasTbl %>% filter( ptid == 'aeras_7' & timePoint == 0 & cd == "8" )
if( testRow1$Gn2pTn17n != ( 0.0085 + 0.014 ) ) stop( "aerasTbl error")


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

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