Compile a list of comparisons — makeListOfComparisons • einprot

Construct a list defining the pairwise group comparisons that will be performed.

makeListOfComparisons(
  allGroups,
  comparisons,
  mergeGroups = list(),
  allPairwiseComparisons,
  ctrlGroup,
  discardGroup = NULL
)

Arguments

allGroups: Character vector containing all group labels in the dataset.
comparisons: List of length-2 character vectors defining comparisons to perform. The first element of each vector represents the denominator of the comparison, the second the numerator. If comparisons is non-empty, ctrlGroup and allPairwiseComparisons are ignored. If one of the two elements in the vector is "complement", it will be created as the complement of the other group.
mergeGroups: Named list defining groups to merge. Each entry of the list corresponds to a new group, and consists of a vector with the original group names (a subset of allGroups). Only comparisons contrasting non-overlapping sets of groups will be performed.
allPairwiseComparisons: Logical scalar, whether all pairwise comparisons shall be performed.
ctrlGroup: Character scalar defining the sample group to use as control group in comparisons.
discardGroup: Character vector. Any comparison including any of these groups will be discarded.

Value

A list with two elements:

comparisons - a list of vectors of length 2, indicating the pairwise group comparisons.
groupComposition - a list specifying the composition of each group label used in comparisons, in terms of the original group names. This is used to keep track of the composition of merged groups.

Author

Charlotte Soneson

Examples

## Perform all pairwise comparisons
makeListOfComparisons(allGroups = c("g1", "g2", "g3"),
                      comparisons = list(), mergeGroups = list(),
                      allPairwiseComparisons = TRUE,
                      ctrlGroup = "g1")
#> $comparisons
#> $comparisons$g2_vs_g1
#> [1] "g1" "g2"
#> 
#> $comparisons$g3_vs_g1
#> [1] "g1" "g3"
#> 
#> $comparisons$g3_vs_g2
#> [1] "g2" "g3"
#> 
#> 
#> $groupComposition
#> $groupComposition$g1
#> [1] "g1"
#> 
#> $groupComposition$g2
#> [1] "g2"
#> 
#> $groupComposition$g3
#> [1] "g3"
#> 
#> 

## Pre-specify the comparisons
makeListOfComparisons(allGroups = c("g1", "g2", "g3"),
                      comparisons = list(c("g1", "g3")),
                      mergeGroups = list(),
                      allPairwiseComparisons = TRUE,
                      ctrlGroup = "g1")
#> $comparisons
#> $comparisons$g3_vs_g1
#> [1] "g1" "g3"
#> 
#> 
#> $groupComposition
#> $groupComposition$g1
#> [1] "g1"
#> 
#> $groupComposition$g2
#> [1] "g2"
#> 
#> $groupComposition$g3
#> [1] "g3"
#> 
#> 

## Compare each group to its complement
makeListOfComparisons(allGroups = c("g1", "g2", "g3"),
                      comparisons = lapply(c("g1", "g2", "g3"),
                                           function(g) c("complement", g)),
                      mergeGroups = list(),
                      allPairwiseComparisons = TRUE,
                      ctrlGroup = "")
#> $comparisons
#> $comparisons$g1_vs_g1_complement
#> [1] "g1_complement" "g1"           
#> 
#> $comparisons$g2_vs_g2_complement
#> [1] "g2_complement" "g2"           
#> 
#> $comparisons$g3_vs_g3_complement
#> [1] "g3_complement" "g3"           
#> 
#> 
#> $groupComposition
#> $groupComposition$g1
#> [1] "g1"
#> 
#> $groupComposition$g2
#> [1] "g2"
#> 
#> $groupComposition$g3
#> [1] "g3"
#> 
#> $groupComposition$g1_complement
#> [1] "g2" "g3"
#> 
#> $groupComposition$g2_complement
#> [1] "g1" "g3"
#> 
#> $groupComposition$g3_complement
#> [1] "g1" "g2"
#> 
#>