# A probabilistic algorithm for matching and comparing multiple flow cytometry samples

## Documentation for package ‘flowMap’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

flowMatch-package | Flow cytometry data cross-sample comparison
crossMap-class | Statistics of mapping the test samples and the reference sample (or the proxy reference)
FRmapping | Multiple sample comparison with a user-defined reference
FRmappingSimple | Multiple sample comparisons
FRstats-class | FR statistics and p-values generated from one single draw of the population pair comparison
FRvalsPerm-class | Statistics generated from the permuted distribution of the observed FR statistics
getCrossList | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getCrossList-method | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFR | F-R test for one population comparison
getFRest | F-R statistic estimates across two samples
getFRmapPnorms | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmapPnorms-method | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmapPnulls | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmapPnulls-method | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmapStats | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmapStats-method | Statistics of mapping the test samples and the reference sample (or the proxy reference)
getFRmat | F-R tests for two-sampbetween two samples
getFRstats | FR statistics and p-values generated from one single draw of the population pair comparison
getFRstats-method | FR statistics and p-values generated from one single draw of the population pair comparison
getFRvalsPerm | Compute statistics for the empirical distribution
getMatched | Identify matched population pairs
getMatchMat | Matching information about a single cross-sample comparison
getMatchMat-method | Matching information about a single cross-sample comparison
getMatchPairs | Matching information about a single cross-sample comparison
getMatchPairs-method | Matching information about a single cross-sample comparison
getNewPops | Data and summary information of the proxy reference sample
getNewPops-method | Data and summary information of the proxy reference sample
getPairList | Information required to making a proxy reference sample
getPairList-method | Information required to making a proxy reference sample
getPnorm | FR statistics and p-values generated from one single draw of the population pair comparison
getPnorm-method | FR statistics and p-values generated from one single draw of the population pair comparison
getPnulls | Statistics generated from the permuted distribution of the observed FR statistics
getPnulls-method | Statistics generated from the permuted distribution of the observed FR statistics
getPopFilt | List of population pairs to be compared during multiple-sample comparisons
getPopFilt-method | List of population pairs to be compared during multiple-sample comparisons
getRefData | Data and summary information of the proxy reference sample
getRefData-method | Data and summary information of the proxy reference sample
getSampleInfo | List of directories and sample files
getSampleInfo-method | List of directories and sample files
getSomePops | Make prefiltering matrix for each test sample
getWnulls | Statistics generated from the permuted distribution of the observed FR statistics
getWnulls-method | Statistics generated from the permuted distribution of the observed FR statistics
makeCrossMap | Make mapping information for the meta set of populations
makeRefMap | Make mapping information for the proxy reference sample
makeRefSample | Make a proxy reference sample
makeSampleInfo | Prepare background files to downstream data processing
matchMat-class | Matching information about a single cross-sample comparison
permutePops | Permute cell population labels across two samples
refMap-class | Information required to making a proxy reference sample
refSample-class | Data and summary information of the proxy reference sample
SampleInfo-class | List of directories and sample files
somePops-class | List of population pairs to be compared during multiple-sample comparisons
statCrossLists | summary statistic across elements of lists