# A toolkit for performing KNN-based statistics for flow and mass cytometry data

## Documentation for package ‘Sconify’ version 1.33.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

AddTsne | Add tSNE to your results.
bz.gmcsf.final | Bodenmiller-Zunder GM-CSF post-SCONE final data
bz.gmcsf.final.norm.scale | Bodenmiller-Zunder GM-CSF post-SCONE final data, that's been quantile normalized and z scored.
exist | Random musing
FcsToTibble | Takes a file as input and returns a data frame of cells by features
Fnn | Compute knn using the fnn algorithm
funct.markers | Functional markers from the Wanderlust dataset.
GetKnnDe | Get the KNN density estimaion
GetMarkerNames | Takes in an example file as input and returns all marker names
Impute | Imputes values for all markers (used as input) for each cell
ImputeTesting | Impute testing
input.markers | Input markers for the Wanderlust dataset
LogTransformQ | Log transform the q values
MakeHist | make.hist
MakeKnnList | Make list of cells by features for each KNN member
markers | Markers for the Wanderlust dataset
MeaningOfLife | Meaning of life
MultipleDonorStatistics | Runs a t test on the medians or means of multiple donors for the same condition
ParseMarkers | Parse markers contained in a Sconify-directed marker file
PostProcessing | Post-processing for scone analysks.
ProcessMultipleFiles | Converts multiple files into a concatenated data frame
QCorrectionThresholding | Corrects all p values for multiple hypotheses, sets threshold for which change values should be reported
QuantNormalize | Performs quantile normalization on the data frame (patient) of interest
QuantNormalizeElements | Takes a list of tibbles as input, and performs per-column quantile normalization, then outputs the quantile normalized list
RunStatistics | Performs a series of statistical tests on the batch of cells of interest.
SconeValues | Master function for per-knn statistics functionality, integrating the other non-exported functions within this script.
SplitFile | Runs "process.multiple.files" on a single file, splits it randomly, and presends half of it is "unstim" and half of it is "stim"
StringToNumbers | Transform strings to numbers.
SubsampleAndTsne | Subsample data and run tSNE
TsneVis | Plot a tSNE map colored by a marker of interest
wand.combined | Wanderlust data combined basal and IL7 cells
wand.final | Post-scone output of the "combiend" Wanderlust data.
wand.ideal.k | A named vector to help the user determine the ideal k for the Wanderlust dataset.
wand.il7 | Wanderlust IL7 data
wand.scone | Wanderlust scone output