CellCounts {COMPASS} | R Documentation

## Compute Number of Cells Positive for Certain Cytokine Combinations

### Description

Compute the number of cells expressing a particular combination of markers for each sample.

### Usage

    CellCounts(data, combinations)

### Arguments

`data` | Either a `COMPASSContainer`, or a list of matrices. Each matrix `i` is of dimension `N_i` cells (rows) by `K` common markers (columns).
`combinations` | A list of 'combinations', used to denote the subsets of interest. See the examples for usage.

### See Also

`Combinations`

### Examples

    set.seed(123)
    ## generate 10 simulated matrices of flow data
    K <- 6 ## number of markers
    data <- replicate(10, simplify=FALSE, {
      m <- matrix( rnorm(1E4 * K, 2000, 1000 ), ncol=K )
      m[m < 2500] <- 0
      colnames(m) <- c("IL2", "IL4", "IL6", "Mip1B", "IFNg", "TNFa")
      return(m)
    })
    names(data) <- sample(letters, 10)
    head( data[[1]] )

    ## generate counts over all available combinations of markers in data
    str(CellCounts(data)) ## 64 columns, as all 2^6 combinations expressed

    ## generate marginal counts
    combos <- list(1, 2, 3, 4, 5, 6) ## marginal cell counts
    cc <- CellCounts(data, combos)

    ## a base R way of doing the same thing
    f <- function(data) {
      do.call(rbind, lapply(data, function(x) apply(x, 2, function(x) sum(x > 0))))
    }
    cc2 <- f(data)

    ## check that they're identical
    stopifnot(identical( unname(cc), unname(cc2) ))

    ## We can also generate cell counts by expressing various combinations
    ## of markers (names) in the data.

    ## count cells expressing IL2 or IL4
    CellCounts(data, "IL2|IL4")

    ## count cells expressing IL2, IL4 or IL6
    CellCounts(data, "IL2|IL4|IL6")

    ## counts for each of IL2, IL4, IL6 (marginally)
    CellCounts(data, c("IL2", "IL4", "IL6"))

    ## counts for cells that are IL2 positive and IL4 negative
    CellCounts(data, "IL2 & !IL4")

    ## expressing the same intent with indices
    CellCounts(data, list(c(1, -2)))

    ## all possible combinations
    str(CellCounts(data, Combinations(6)))

    ## can also call on COMPASSContainers
    data(COMPASS)
    CellCounts(CC, "M1&M2")

[Package COMPASS version 1.16.2 Index]