getFRmat: FR tests to compare two flow cytometry samples

In jhsiao999/flowMap: Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test

Description

Perform FR tests to compare cell populations across two flow cytometry samples. The FR statistics are estimated based on a downsampling scheme designed to optimize runtime as well as precision and accuracy of the statistics. The downsampling scheme samples from the pooled data of events across a single cell population comparison. The events in the sample maintain the same cell population membership ratio as the events in the pooled data (proportional) or include an equal number of events from the two cell populations in the comparison.

Usage

getFRmat(XX1, XX2, sampleMethod, sampleSize, i = NULL)

Arguments

XX1	a flow cytometry sample of cell populations, organized in a matrix or a data.frame of events (rows) by features (columns) where cell populaiton memberships are indexed in the last column by a variable named id.
XX2	a flow cytometry sample of cell populations, organized in a matrix or a data.frame of events (rows) by features (columns) where cell populaiton memberships are indexed in the last column by a variable named id.
sampleMethod	downsampling method, options include equalSize or proportional. Both methods sample events without replacement from the combined events in a single cell population pair comparison. Using equalSize, each sample includes an equal number of events from the two cell populations being compared. Using proportional, the ratio of the event membership is same as the ratio of event membershiop prior to sampling. (default: proportional)
sampleSize	specifies S,the number of events to be included in each sample. For equalSize sampling , S/2 is sampled from each population. For proportional sampling, the ratio of event membership is the same as the ratio of event membership prior to sampling.
i	dummy variable to initialize parallel computing (doParallel).

Value

wmat a list of matrices containing sample FR statistics for each XX1 by XX2 population comparisons.

runsmat a list of matrices containing sample runs for each XX1 by XX2 population comparisons.

mumat a list of matrices containing sample expected number of runs for each XX1 by XX2 population comparisons.

sigma2mat a list of matrices containing sample estimated variance of runs for each XX1 by XX2 population comparisons.

pNormat a list of matrices containing sample one-sided p-value associated with the FR statistics of XX1 by XX2 population comparisons under the asymptotic normality assumption of the FR statistic.

Author(s)

Chiaowen Joyce Hsiao [e-mail]

jhsiao999/flowMap documentation built on May 19, 2019, 9:28 a.m.