# Extract and Analyze Median Molecule Intensity from 'citrus' Output

## Documentation for package ‘mineCitrus’ version 1.0.0

- DESCRIPTION file

## Help Pages

allmeds | Gets matrices of medians for each individual sample for all measured parameters for all clusters
citrus.combinedFCSSet | Cytometry data set for example of Citrus data set from nolanlab/citrus
citrus.foldClustering | Clustering data for example of Citrus data set from nolanlab/citrus
citrus.foldFeatureSet | Correlation data for example of Citrus data set from nolanlab/citrus
classclustermeds | Gets matrices of medians for each individual sample for all measured parameters for all clusters
clustermeds | Gets matrix of medians for desired measured features for all clusters meeting threshold requirements specified in Citrus
difMarkerPlots | Plot dot plots of features where both clusters are significantly different from the reference cluster without processing data before hand
difMarkerPlots2 | Plot dot plots of features where one cluster is significantly different from the reference cluster without processing data before hand
filterMarker | Filters list of data matrices with columns corresponding to the measured parameters of interest
findclust | Filters list to contain only desired clusters
findSig | Assesses significance of ANOVA and t-test results
plotdif | Plot dot plots of features where both clusters are significantly different from the reference cluster
plotdif2 | Plot dot plots of features where one cluster is significantly different from the reference cluster
posthoc | Runs ANOVA and t-tests comparing clusters and markers in clusters
processforanova | Processes cluster signaling data in form for statistical analysis
sortmat | Reorders to rows (corresponding to different clusters) of a matrix of medians to a desired order