SconeValues {Sconify} | R Documentation

## Master function for per-knn statistics functionality, integrating the other non-exported functions within this script.

### Description

This function is run following the KNN computation and respective cell grouping. The function also contains a progress ticker that allows one to determine how much time left in this function.

### Usage

    SconeValues(nn.matrix, cell.data, scone.markers, unstim, threshold = 0.05,
      fold = "median", stat.test = "mwu", multiple.donor.compare = FALSE)

### Arguments

`nn.matrix` | a matrix of cell index by nearest neighbor index, with values being cell index of the nth nearest neighbor
`cell.data` | tibble of cells by features
`scone.markers` | vector of all markers to be interrogated via statistical testing
`unstim` | an object (used so far: string, number) specifying the "basal" condition
`threshold` | a number indicating the p value the raw change should be thresholded by.
`fold` | a string that specifies the use of "median" or "mean" when calculating fold change
`stat.test` | string denoting Mann Whitney U test ("mwu") or T test ("t)
`multiple.donor.compare` | a boolean that indicates whether t test across multiple donors should be done

### Value

result: tibble of raw changes and p values for each feature of interest, and fraction of cells with condition 2

### Examples

    ex.nn <- Fnn(wand.combined, input.markers)
    SconeValues(ex.nn, wand.combined, funct.markers, "basal")

[Package Sconify version 1.12.0 Index]