Man pages for ParkerICI/premessa
R package for pre-processing of flow and mass cytometry data

as_flowFrameConvert a matrix to a flowFrame object
calculate_baselineCalculate baseline for normalization
calculate_bcs_separationThis assumes that all barcodes are identified by the same...
copy_keywordsCopy FCS keywords from a source to a target flowFrame object
correct_data_channelsNormalize data
debarcode_dataDebarcodes data by doing normalization after preliminary...
debarcode_data_matrixDebarcodes an individual matrix of data
debarcode_fcsMain wrapper for the debarcoder pipeline.
debarcoder_GUIStarts the debarcoder GUI
get_assignments_at_thresholdAssign events to a specific sample
get_barcode_channels_namesGet the names of the barcode channels
get_mahalanobis_distanceCalculates the squared Mahalanobis distance from the centroid...
get_mahalanobis_distance_from_beadsCalculates the Mahalanobis distance of each event from the...
get_sample_idxReturns the indices of the events corresponding to a given...
get_well_abundancesCalculate number of events assigned to each sample
identify_beadsBeads identification
normalize_by_popNormalize the barcode channels
normalize_folderNormalize a folder of FCS files
normalizer_GUIStarts the normalizer GUI
plot_all_barcode_biaxialsScatteplot matrix of all the barcode channels
plot_barcode_channels_intensitiesPlotting barcode channels intensities for individual events
plot_barcode_separationPlotting debarcoded sample yields as a function of the...
plot_barcode_yieldsPlotting sample yields after debarcoding
plot_distance_from_beadsBiaxial plot color-coded according to the Mahalanobis...
plot_separation_histogramPlotting the distribution of separation values
premessapremessa: A package for normalization and debarcoding of...
read_barcode_keyLoading a barcode key
read_parametersRead parameters from a set of FCS files
remove_beads_from_fcsRemove beads from a flowFrame object
remove_beads_from_fileRemove beads from an FCS file
rename_fcs_parameters_descRename FCS parameter descriptions
rename_fcs_parameters_nameRename FCS parameter names
rename_parameters_in_filesRenames FCS parameters in a set of files
write_flowFrameWrite a flowFrame as FCS file
ParkerICI/premessa documentation built on Oct. 6, 2017, 3:25 a.m.