Calculate TRI

Calculate_TRI calculates the Titer Response Index (TRI)

Calculate_TRI(dat_list, subjectCol = "SubjectID", discretize = c(0.2, 0.3),
  responseLabels = paste0(c("low", "moderate", "high"), "Responder"),
  na_action = "na.fail", ...)

Arguments

dat_list	a named list like the one returned by FormatTiters.
subjectCol	the name of the column specifying a subject ID. Default is "SubjectID".
discretize	a vector of quantiles in (0, 0.5] specifying where to make the cutoff for low, moderate and high responses. Default is 20% and 30%.
responseLabels	names for low, moderate and high responses
na_action	how should missing NA values be treated. Default is "na.fail"
...	Additional arguments passed to lm

Details

Calculates the Titer Response Index (TRI) defined in Bucasas et al. 2011 Missing (NA) values are handled by being returned as missing in the endpoints in the output

References

Bucasas KL, et al. (2011) Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans. J Infect Dis 203(7):921-9.

See also

lm

Examples

## Prepare the data
titer_list <- FormatTiters(Year2_Titers)
#> - Log transforming Pre and Post columns
#> - Setting any negative log fold changes to 0

## Calculate the titer response index (TRI)
endpoints <- Calculate_TRI(titer_list)
summary(endpoints)
#>                Length Class      Mode   
#> models           3    -none-     list   
#> residualMatrix 207    -none-     numeric
#> scores           4    data.frame list   
#> TRI             69    -none-     numeric
#> TRI_d20         69    factor     numeric
#> TRI_d30         69    factor     numeric

## Get discrete endpoints using upper/lower 30%
endpoints$TRI_d30
#>            110191            110192            110193            110194 
#> moderateResponder      lowResponder moderateResponder      lowResponder 
#>            110195            110196            110197            110198 
#> moderateResponder      lowResponder     highResponder moderateResponder 
#>            110199            110200            110201            110202 
#>      lowResponder     highResponder moderateResponder moderateResponder 
#>            110203            110204            110205            110207 
#> moderateResponder moderateResponder     highResponder      lowResponder 
#>            110208            110209            110210            110211 
#>      lowResponder      lowResponder      lowResponder moderateResponder 
#>            110212            110213            110214            110215 
#> moderateResponder moderateResponder      lowResponder      lowResponder 
#>            110216            110241            110242            110243 
#>     highResponder moderateResponder moderateResponder      lowResponder 
#>            110244            110245            110247            110248 
#>     highResponder     highResponder     highResponder moderateResponder 
#>            110250            110251            110252            110253 
#> moderateResponder     highResponder moderateResponder     highResponder 
#>            110254            110255            110256            110257 
#> moderateResponder     highResponder     highResponder     highResponder 
#>            110258            110259            110260            110261 
#> moderateResponder     highResponder      lowResponder     highResponder 
#>            110262            110263            110264            110265 
#> moderateResponder moderateResponder      lowResponder     highResponder 
#>            110266            110267            110268            110269 
#>     highResponder     highResponder     highResponder     highResponder 
#>            110270            110271            110272            110273 
#> moderateResponder moderateResponder     highResponder moderateResponder 
#>            110274            110275            110276            110277 
#>      lowResponder      lowResponder moderateResponder     highResponder 
#>            110278            110279            110280            110281 
#>      lowResponder      lowResponder moderateResponder      lowResponder 
#>            110282            110283            110284            110285 
#> moderateResponder moderateResponder      lowResponder      lowResponder 
#>            110286 
#>      lowResponder 
#> Levels: lowResponder moderateResponder highResponder

## Recreate Supp. Fig. S1
pairs(endpoints$scores, col = endpoints$TRI_d30)