Man pages for markdane/MEMA
Functions to preprocess and normalize MEMA data
| addBarcodes | Add in the barcodes the MEPs came from |
| addOmeroIDs | Add the URLs for the Omero IDs on the OHSU Omero server |
| addPolarCoords | Add local XY and polar coordinates |
| addSpotProportions | Add the porportions of gated cells in the spot populations |
| boundedLog2 | Utility function that returns log2 with lower non-infinite... |
| boundedLogit | Utility function that returns logit with lower and upper... |
| calc2NProportion | Calculate the proportion of cells that are classfied as... |
| calcAdjacency | Add measures of adjacency based on cell positions in the... |
| calcProportion | Calculate the proportion of x that are TRUE |
| calcQAScore | Calculate a QA score for MEMAs |
| calcResidual | Calculate the residuals from the median of a vector of... |
| calcTheta | Calculate the polar coordinate theta value |
| cellNeighbors | Count the number of neigbors around a nuclei |
| cleanColumnNames | Change the periods in the column names to spaces |
| cleanCommonSignalDt | Clean the common signal datatable |
| cleanLegacyIssues | Clean up issues that have been problems in previous pipelines |
| combineSignals | Combine the common signals into a datatable |
| compressHA | Replace the long names for hyaluronic acid with abbreviations |
| convertColumnNames | Convert column names in a data.table |
| create8WellHistograms | Create histograms of 8 well MEMA data |
| create8WellPseudoImage | Create pseudeoimages of 8 well MEMA data |
| createRUVM | Create an M matrix for the RUV normalization |
| CV | Calculate Coefficient of Variation (CV) |
| findPerimeterCell | 'findPerimeterCell' Determine the perimeter cell in wedge |
| formatCP96Well | Format 96 well plate raw data from the Cell Profiler Pipeline |
| gateCells | Gate cells based on specific stains if they are in the... |
| gateOnlocalMinima | Gate a vector on a local minima |
| gateOnQuantile | Gate values at a specific quantile |
| getBarcodes | Get barcodes from the Synapse Plate Tracker files |
| getCPData | Get the data from the Cell Profiler pipeline |
| getICData | Read and convert INCell data to CP format |
| getLogMetadata | Get deposition values from an Aushon log dta files |
| getMetadata | Get metadata from either An! or !An! files |
| getOmeroIDs | Read in and merge the Omero URLs |
| getSpotLevelData | Get the spot level data for a study |
| getSpotMetadata | Read the spot metadata from a gal file |
| getWellMetadata | Read the well metadata from a multi-sheet Excel file |
| kmeansCluster | kMeans cluster an intensity value |
| kmeansClusterValue | Cluster using kmeans |
| labelOuterCells | Classify Outer cells |
| localMinima | Find a local minima appropriate for classiying a vector of... |
| loessModel | Create a median normalized loess model of an array |
| loessNorm | Loess normalize an array using the spatial residuals |
| loessNormArray | Loess normalize values within an array |
| logIntensities | Wrapper function to log intensity values in a data.table |
| medianNorm | Median normalize a vector |
| mergeSpot8WellMetadata | Create a single datatable for all wells in an 8 well plate... |
| mergeSpot96WellMetadata | Merge the spot well level metadata for a 96 well plate |
| normRUVLoessResiduals | Apply RUV and Loess Normalization to the signals in a MEMA... |
| numericMedian | Return the median of a vector as a numeric value |
| plotLEHmap | Plot a heatmap with ligand rows and ECM protein columns |
| plotSCCHeatmapsQAHistograms | Print pseudoimages and histograms of the spot cell count... |
| preprocessCommonSignalsLevel3 | Normalize the common signals across studies |
| preprocessLevel4 | Summarize spot level data to the MEP level |
| processan2omero | Process the metadata in an an2omero file |
| QASpotData | QA the spot level data |
| QASpotLevelData | Add QA flags to the spot level data |
| readLogData | Read in and parse an Aushon XML log file |
| readMetadata | Read metadata from a multi-sheet excel file |
| readSpotMetadata | Read the spot metadata from a gal file |
| rotateMetadata | Rotate the metadata 180 degrees in Array space |
| RUVArrayWithResiduals | Apply RUV normalization on a signal and its residuals |
| RUVIII | RUV normalization function |
| se | Omit na values if present |
| signalResidualMatrix | Generate a matrix of signals and residuals |
| spotNormIntensities | Add spot level normalizations for median intensities |
| summarizeToSpot | Summarize cell level data to the spot level |
| wellAN | Returns a character vector of alphanumeric well names |
| writeCellLevel | Write the cell level raw data and metadata Level 1 data. |
