# MetaCyto: A package for meta-analysis of cytometry data

## Documentation for package ‘MetaCyto’ version 1.12.0

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

## Help Pages

autoCluster.batch | Cluster the preprocessed fcs files from different studies in batch
clusterStats | Derive summary statistics for clusters
collectData | Collect and combine data from multiple csv files of the same format
densityPlot | Draw density plot for each cell cluster.
fcsInfoParser | Organize fcs files in a study from ImmPort into panels
filterLabels | Filter cluster labels
findCutoff | Find cutoff for a 1D distribution
flowHC | Cluster cytometry data using hierarchical clustering
flowSOM.MC | Cluster cytometry data using FlowSOM
glmAnalysis | Perform generalized linear model analysis to estimate effect size.
labelCluster | Label each cluster as "+" or "-" or neutral for each marker
labelSummary | Make a summary for the labels (cell populations) identified in different cytometry panels.
markerFinder | Find markers in a flow frame object
metaAnalysis | Performs meta-analysis
nameUpdator | Used to update marker names
panelSummary | Summarize markers in panels.
plotGA | Plot the result from the glmAnalysis function
preprocessing | Preprocess fcs files from a single experiment
preprocessing.batch | Preprocessing fcs files from different studies in batch.
sampleInfoParser | Collect sample information for fcs files in a study from ImmPort.
searchCluster | Search for clusters using pre-defined labels
searchCluster.batch | Search for clusters using pre-defined labels in cytometry data from different studies in batch
set2Frame | Combine cells in a flow set into a flow frame.