Calculate COMPASS-derived overall responder probability — response

Calculate the probability of responding to at least one cytokine combination, assuming independence of the probability estimates between cytokine combinations.

Usage

response_prob(c_obj, exc = NULL)

Arguments

c_obj: object of class 'COMPASSResult'. The posterior probabilities for individual cytokine combinations are obtained here.
exc: character vector. Specifies cytokine combination(s) to exclude. If NULL, then none except the all-negative population are excluded. Default is NULL.

Value

A dataframe with columns sampleid and prob.

Details

Calculates the probability of an individual responding to at least one cytokine combination as (1-product((1-prob_i))), where prob_i is the probability of responding to the i-th cytokine combination and the product is taken over all cytokine combinations except the all-negative cytokine combination.

Examples

data("c_obj", package = "UtilsCompassSV")
response_prob(c_obj = c_obj)
#> # A tibble: 148 × 2
#>    sampleid     prob
#>    <chr>       <dbl>
#>  1 010673_D0   1    
#>  2 010782_D0   1    
#>  3 010782_D720 1    
#>  4 010978_D0   1    
#>  5 010993_D0   1    
#>  6 020185_D0   1    
#>  7 030442_D0   1    
#>  8 030448_D0   1    
#>  9 030545_D0   1    
#> 10 030697_D0   0.521
#> # ℹ 138 more rows
response_prob(
  c_obj = c_obj,
  exc = c(
    "IFNg&IL2&TNF&!IL17&!IL6&!IL22",
    "IFNg&!IL2&TNF&!IL17&!IL6&!IL22"
  )
)
#> # A tibble: 148 × 2
#>    sampleid     prob
#>    <chr>       <dbl>
#>  1 010673_D0   1    
#>  2 010782_D0   0.992
#>  3 010782_D720 0.996
#>  4 010978_D0   1    
#>  5 010993_D0   1    
#>  6 020185_D0   0.998
#>  7 030442_D0   1    
#>  8 030448_D0   1    
#>  9 030545_D0   0.897
#> 10 030697_D0   0.521
#> # ℹ 138 more rows