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

Description Usage Arguments Value Author(s)

View source: R/makeDistmat.r


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).


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



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).


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)


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)


number of random samples. Runtime is linear in the number of random samples. (default: 200)


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.


Chiaowen Joyce Hsiao [email protected]

flowMap documentation built on May 2, 2018, 2:03 a.m.