makeDistmat: Generate a similarity matrix quantifying similarity between...

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

Description

Perform getFRest for multiple sample comparisons. For a two-sample comparison of n1 and n2 cell populations, we generate a similarity matrix of dimension (n1+n2)-by-(n1+n2).

Usage

makeDistmat(samples, sampleMethod = "proportional", sampleSize = 200,
  ndraws = 200)

Arguments

samples	a list of data.frames or matrices of flow cytometry samples. Each data.frame or matrix consists of columns of features (flow cytometry channels), followed by a column of population membership (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. (default: 200)
ndraws	number of random samples. Runtime is linear in the number of random samples. (default: 200)

Value

distmat a matrix of estimated FR statistics across multiple samples. Rows and columns are indexed in the order in which each sample appears in the input list. For example, a two sample comparison entails rows and columns of distmat indexed as 1.x follwed by 2.y where x is the Sample 1 population IDs, and 2.y is the Sample 2 population IDs.

Author(s)

Chiaowen Joyce Hsiao [e-mail]

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