flowSet2LongDf: Convert a flowSet to one long dataframe with all identifiers...

In jtheorell/flowSpecs: Tools for processing of high-dimensional cytometry data

Convert a flowSet to one long dataframe with all identifiers as separate #columns.

Description

This function is mainly used for compatibility with matrix-based clustering algorithms, such as depeche in the DepecheR package.

Usage

flowSet2LongDf(flowObj, idInfo)

Arguments

flowObj	The flowSet or flowFrame to be converted to a dataframe.
idInfo	A list of any number of characteristics that can be derived from the file names. For each entry, a gsub specification of where to find the information in the file name should be added, such as id=""..._|..."".

Value

A long data frame with one column per PMT/APD (or fluorochrome, depending on the state of the imported files), one for the acquisition date (for fcs files) and one colum for each specified slot above. If no gsub-pattern is provided, only a single column with the full file name will be used to separate the observations from each file.

See Also

depeche

Examples

#' # Load uncompensated data
data(fullPanel)

# Load the spectral unmixing matrix generated with controls from the same
# experiment. These can be generated using the specMatCalc function.
data(specMat)

# Now unmix
fullPanelUnmix <- specUnmix(fullPanel, specMat)

# Transform all fluorescent channels
fullPanelTrans <- arcTrans(fullPanelUnmix,
    transNames = colnames(fullPanelUnmix)[6:18])

# This function is primarily meant to be used with flowSets.
# If we had only one flowFrame, we could just extract the data by
# the use of the flowCore function exprs(), so we will convert the data to a
# flowSet now.
library(flowCore)
fullPanelFs <- flowSet(fullPanelTrans)

# Before converting to a dataframe it is important to get an idea of the
# structure of the names, to be able to extract meaningful parts of the name.
# Here, we have an exceptional case again, as the flowSet has just been
# created, so there is actually no meaningful name of the flowFrame inside
# it. So for example reasons, we will give it one now:
sampleNames(fullPanelFs) <- "PBMC_full_panel_d1.fcs"

# And now, we generate the dataframe:
fullPanelDf <- flowSet2LongDf(fullPanelFs, idInfo =
                                 list("Tissue" = "|_full_panel_..\\.fcs",
                                     "Donor" = "...._full_panel_|\\.fcs"))
# This is the result
str(fullPanelDf)

jtheorell/flowSpecs documentation built on April 24, 2023, 2:59 a.m.