Package index • USERM

All functions

AddRes2Userm(): Add a Res object to a Userm object

AddScale(): Add scaling parameters for a specific fluorophore

B_remove_outlier(): Remove outliers from a data frame column using a MAD-based robust filter

checkRes_covMtx(): Visualize Covariance Matrix at a Specific Bin

checkRes_covScatter(): Plot Covariance Scatter Between Two Detectors with Regression Line

checkRes_interceptMtx(): Visualize the Intercept Matrix from a Result Object

checkRes_slopMtx(): Visualize the Slope Matrix from a Result Object

checkSig_linePlot(): Plot Signature Signal Line for a Given ID

check_ss(): Compute Spillover Spreading Score (SS) Between Fluorophores

correct_to_horizontal(): Remove linear trend from Y relative to X

CreateRes(): Create a Res object

CreateUserm(): Create a userm object

create_seq(): Generate a numeric sequence based on a scaling method

EllipseLine_intersection(): Compute Intersection Points Between an Ellipse and a Line

EstimateCoefMtx(): Estimate Coefficient Matrix of Slope Components in USERM

EstimateDistance(): Estimate Elliptical Distance Between Two USERM Spread Objects

EstimateHotspotMtx(): Estimate Hotspot Matrix

EstimateSimilarityMtx(): Estimate Cosine Similarity Matrix for Fluorochromes

EstimateSpread(): Estimate Signal Spread for a Given Population

EstimateSSM(): Estimate Spillover Spreading Matrix (SSM) from Unmixing and Control Data

ExtractSig(): Extract a normalized signature from a single-stained control (SCC)

ExtractSSM(): Extract Spillover Spreading Matrix (SSM) related object from Positive and Negative Controls

getColor(): Interpolate a color based on a numeric value

getRes(): Retrieve Result Object by ID

getSigMtx(): Retrieve Signature Matrix by ID

PredIsobandPlot(): Generate a prediction plot of unmixed spread using isobands or contour lines

PredIsobandPlotMulti(): Overlay Prediction Grids Using Isobands or Contour Lines

PredMultipleSpread(): Launch an interactive Shiny app to explore predicted spread for multiple populations

PredOneSpread(): Launch an interactive Shiny app to explore predicted spread

querySig(): Query and summarize Signature list information

RenameFluor(): Rename a fluorophore in a Userm object

robust_pairwise_cov_zscore(): Robust Pairwise Covariance Matrix Using Z-score Outlier Removal

scale_z(): Scale Z Values with Cumulative Threshold Filtering

SigList2df(): Convert a list of signature objects into a data frame

SlopEstimation(): Estimate slope and intercept matrices from residuals

Userm_html_table(): Generate an HTML table with color-coded cells and a legend

Vis_Mtx(): Visualize a Matrix as a Heatmap with Custom Colors and Labels

vis_ss_scatter(): Visualize Spillover Spreading Between Fluorophores