prepareCellData {cydar} | R Documentation

## Prepare mass cytometry data

### Description

Convert single-cell marker intensities from a mass cytometry experiment into a format for efficient counting.

### Usage

    prepareCellData(x, markers=NULL, ...)

### Arguments

`x` | A named list of numeric matrices, where each matrix corresponds to a sample and contains expression intensities for each cell (row) and each marker (column). Alternatively, a ncdfFlowSet object containing the same information.
`markers` | A vector specifying the markers to use in downstream analyses.
`...` | Additional arguments to pass to `buildKmknn`.

### Details

This function constructs a CyData object from the marker intensities of each cell in one or more samples. The `buildKmknn` function is used to precompute internal structures for downstream nearest-neighbour searching.

If `markers` is specified, only the selected markers will be used in the precomputation. This restricts the markers that are used in downstream functions - namely, `countCells` and `neighborDistances`. By default, `markers=NULL` which means that all supplied markers will be used.

Markers that are not in `markers` will be ignored in distance calculations. However, their intensities are still stored in the output object, for use in functions like `medIntensities`.

### Value

A CyData object with no rows and the number of columns equal to the number of samples in `x`. Sample names are stored as the column names of the output object. Precomputed values for internal use are stored in the `"cydar"` field of the `metadata` slot.

### Author(s)

Aaron Lun

### See Also

`countCells`, `neighborDistances`

### Examples

    ### Mocking up some data: ###
    nmarkers <- 20
    marker.names <- paste0("X", seq_len(nmarkers))
    nsamples <- 8
    sample.names <- paste0("Y", seq_len(nsamples))

    x <- list()
    for (i in sample.names) {
        ex <- matrix(rgamma(nmarkers*1000, 2, 2), ncol=nmarkers, nrow=1000)
        colnames(ex) <- marker.names
        x[[i]] <- ex
    }

    ### Running the function: ###
    cd <- prepareCellData(x)
    cd

[Package cydar version 1.6.1 Index]