Man pages for MEP-LINCS/MEMA
Functions to preprocess and normalize MEMA data

addBarcodesAdd in the barcodes the MEPs came from
addOmeroIDsAdd the URLs for the Omero IDs on the OHSU Omero server
addPolarCoordsAdd local XY and polar coordinates
addSpotProportionsAdd the porportions of gated cells in the spot populations
boundedLog2Utility function that returns log2 with lower non-infinite...
boundedLogitUtility function that returns logit with lower and upper...
calc2NProportionCalculate the proportion of cells that are classfied as...
calcAdjacencyAdd measures of adjacency based on cell positions in the...
calcProportionCalculate the proportion of x that are TRUE
calcQAScoreCalculate a QA score for MEMAs
calcResidualCalculate the residuals from the median of a vector of...
calcThetaCalculate the polar coordinate theta value
cellNeighborsCount the number of neigbors around a nuclei
cleanColumnNamesChange the periods in the column names to spaces
cleanCommonSignalDtClean the common signal datatable
cleanLegacyIssuesClean up issues that have been problems in previous pipelines
combineSignalsCombine the common signals into a datatable
compressHAReplace the long names for hyaluronic acid with abbreviations
convertColumnNamesConvert column names in a data.table
create8WellHistogramsCreate histograms of 8 well MEMA data
create8WellPseudoImageCreate pseudeoimages of 8 well MEMA data
createRUVMCreate an M matrix for the RUV normalization
CVCalculate Coefficient of Variation (CV)
findPerimeterCell'findPerimeterCell' Determine the perimeter cell in wedge
formatCP96WellFormat 96 well plate raw data from the Cell Profiler Pipeline
gateCellsGate cells based on specific stains if they are in the...
gateOnlocalMinimaGate a vector on a local minima
gateOnQuantileGate values at a specific quantile
getBarcodesGet barcodes from the Synapse Plate Tracker files
getCPDataGet the data from the Cell Profiler pipeline
getICDataRead and convert INCell data to CP format
getLogMetadataGet deposition values from an Aushon log dta files
getMetadataGet metadata from either An! or !An! files
getOmeroIDsRead in and merge the Omero URLs
getSpotLevelDataGet the spot level data for a study
getSpotMetadataRead the spot metadata from a gal file
getWellMetadataRead the well metadata from a multi-sheet Excel file
kmeansClusterkMeans cluster an intensity value
kmeansClusterValueCluster using kmeans
labelOuterCellsClassify Outer cells
localMinimaFind a local minima appropriate for classiying a vector of...
loessModelCreate a median normalized loess model of an array
loessNormLoess normalize an array using the spatial residuals
loessNormArrayLoess normalize values within an array
logIntensitiesWrapper function to log intensity values in a data.table
medianNormMedian normalize a vector
mergeSpot8WellMetadataCreate a single datatable for all wells in an 8 well plate...
mergeSpot96WellMetadataMerge the spot well level metadata for a 96 well plate
normRUVLoessResidualsApply RUV and Loess Normalization to the signals in a MEMA...
numericMedianReturn the median of a vector as a numeric value
plotLEHmapPlot a heatmap with ligand rows and ECM protein columns
plotSCCHeatmapsQAHistogramsPrint pseudoimages and histograms of the spot cell count...
preprocessCommonSignalsLevel3Normalize the common signals across studies
preprocessLevel4Summarize spot level data to the MEP level
processan2omeroProcess the metadata in an an2omero file
QASpotDataQA the spot level data
QASpotLevelDataAdd QA flags to the spot level data
readLogDataRead in and parse an Aushon XML log file
readMetadataRead metadata from a multi-sheet excel file
readSpotMetadataRead the spot metadata from a gal file
rotateMetadataRotate the metadata 180 degrees in Array space
RUVArrayWithResidualsApply RUV normalization on a signal and its residuals
RUVIIIRUV normalization function
seOmit na values if present
signalResidualMatrixGenerate a matrix of signals and residuals
spotNormIntensitiesAdd spot level normalizations for median intensities
summarizeToSpotSummarize cell level data to the spot level
wellANReturns a character vector of alphanumeric well names
writeCellLevelWrite the cell level raw data and metadata Level 1 data.
MEP-LINCS/MEMA documentation built on May 20, 2019, 2:47 p.m.