SconeValues: Master function for per-knn statistics functionality,...

In tjburns08/Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data

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")

tjburns08/Sconify documentation built on May 31, 2019, 8:56 a.m.