Summary statistics per channel computation

Computation of summary statistic for selected channels, for all flowFrames of a flowSet, or for all expression matrices of a list. This method provides three different input modes:

• the user provides directly a flowCore::flowSet loaded in memory (RAM)

• the user provides directly a list of expression matrices of which the column names are the channel/marker names

• the user provides (1.) a number of samples nSamples; (2.) an ad-hoc function that takes as input an index between 1 and nSamples, and codes the method to load the corresponding expression matrix in memory;

Usage

channelSummaryStats(
  x,
  loadExprMatrixFUN = NULL,
  loadExprMatrixFUNArgs = NULL,
  channels = NULL,
  statFUNs = stats::median,
  verbose = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  BPOPTIONS = BiocParallel::bpoptions(packages = c("flowCore"))
)

Arguments

x

can be:

• a flowCore::flowSet

• a list of expression matrices (Double matrix with named columns)

• the number of samples (integer >=1)

loadExprMatrixFUN

the function used to translate an integer index into an expression matrix. In other words, the function should code how to load the indexth expression matrix into memory. IMPORTANT: the expression matrix index should be the first function argument and should be named exprMatrixIndex.

loadExprMatrixFUNArgs

(optional) a named list containing additional input parameters of loadExprMatrixFUN()

channels

which channels needs to be included:

• if it is a character vector, it can refer to either the channel names, or the marker names

• if it is a numeric vector, it refers to the indices of channels in fs

• if NULL, all scatter and fluorescent channels of fs #' will be selected.

statFUNs

a list (possibly of length one) of functions to call to calculate the statistics, or a simple function. This list can be named, in that case, these names will be transfered to the returned list.

verbose

if TRUE, output a message after each single statistics calculation

BPPARAM

sets the BPPARAM back-end to be used for the computation. If not provided, will use BiocParallel::SerialParam() (no task parallelization)

BPOPTIONS

sets the BPOPTIONS to be passed to bplapply() function. Note that if you use a SnowParams back-end, you need to specify all the packages that need to be loaded for the different CytoProcessingStep to work properly (visibility of functions). As a minimum, the flowCore package needs to be loaded. (hence the default BPOPTIONS = bpoptions(packages = c("flowCore")) )

Value

a list of named statistic matrices. In each stat matrix, the columns are the channel statistics for all flowFrames of the flowSet. Exception: if only one stat function (and not a list) is passed in statFUNs, the return value is simplified to the stat matrix itself.

Examples

library(CytoPipeline)

data(OMIP021Samples)

# estimate scale transformations 
# and transform the whole OMIP021Samples

transList <- estimateScaleTransforms(
    ff = OMIP021Samples[[1]],
    fluoMethod = "estimateLogicle",
    scatterMethod = "linearQuantile",
    scatterRefMarker = "BV785 - CD3")

OMIP021Trans <- CytoPipeline::applyScaleTransforms(
    OMIP021Samples, 
    transList)

channelsOrMarkers <- c("FSC-A", "SSC-A", "BV785 - CD3")

# calculate mean for each 4 selected channels, for each 2 samples

channelMeans <- channelSummaryStats(
    OMIP021Trans,
    channels = channelsOrMarkers,
    statFUNs = mean)
    
# calculate median AND std deviation
# for each 4 selected channels, for each 2 samples

channelMedians <- channelSummaryStats(
    OMIP021Trans,
    channels = channelsOrMarkers,
    statFUNs = list("median" = stats::median, 
                    "std.dev" = stats::sd))