Computation of summary statistic for selected channels, for all flowFrames of a flowSet. This method provides two different input modes:
the user provides directly a flowSet loaded in memory (RAM).
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 flowFrame in memory;
Optional row and column ranges can be provided to limit the calculation
to a specific rectangle of the matrix. These i.e. can be specified as a way
to split heavy calculations of large distance matrices
on several computation nodes.
channelSummaryStats(
x,
loadFlowFrameFUN = NULL,
loadFlowFrameFUNArgs = NULL,
channels = NULL,
statFUNs = stats::median,
verbose = FALSE,
BPPARAM = BiocParallel::SerialParam(),
BPOPTIONS = BiocParallel::bpoptions(packages = c("flowCore"))
)either a flowCore::flowSet, or the number of samples (integer >=1)
the function used to translate a flowFrame index
into a flowFrame. In other words, the function should code how to load a
specific flowFrame into memory. Important: the flow Frame index should be
the first function argument and should be named ffIndex.
(optional) a named list containing
additional input parameters of loadFlowFrameFUN()
which channels (integer index(ices) or character(s)):
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 indexes of channels in fs
if NULL all scatter and fluorescent channels of fs
will be selected
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 value.
if TRUE, output a message
after each single distance calculation
sets the BPPARAM back-end to
be used for the computation. If not provided, will use
BiocParallel::SerialParam() (no task parallelization)
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")) )
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.
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))