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mineCitrus (version 1.0.0)

Extract and Analyze Median Molecule Intensity from 'citrus' Output

Description

Citrus is a computational technique developed for the analysis of high dimensional cytometry data sets. This package extracts, statistically analyzes, and visualizes marker expression from 'citrus' data. This code was used to generate data for Figures 3 and 4 in the forthcoming manuscript: Throm et al. <80><9c>Identification of Enhanced Interferon-Gamma Signaling in Polyarticular Juvenile Idiopathic Arthritis with Mass Cytometry<80><9d>, JCI-Insight. For more information on Citrus, please see: Bruggner et al. (2014) . To download the 'citrus' package, please see .

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Version

Install

install.packages('mineCitrus')

Monthly Downloads

179

Version

1.0.0

License

GPL-2

Maintainer

Allison Throm

Last Published

July 5th, 2018

Functions in mineCitrus (1.0.0)

clustermeds

Gets matrix of medians for desired measured features for all clusters meeting threshold requirements specified in Citrus
findSig

Assesses significance of ANOVA and t-test results
difMarkerPlots

Plot dot plots of features where both clusters are significantly different from the reference cluster without processing data before hand
filterMarker

Filters list of data matrices with columns corresponding to the measured parameters of interest
allmeds

Gets matrices of medians for each individual sample for all measured parameters for all clusters
classclustermeds

Gets matrices of medians for each individual sample for all measured parameters for all clusters
citrus.foldClustering

Clustering data for example of Citrus data set from nolanlab/citrus
plotdif2

Plot dot plots of features where one cluster is significantly different from the reference cluster
citrus.combinedFCSSet

Cytometry data set for example of Citrus data set from nolanlab/citrus
posthoc

Runs ANOVA and t-tests comparing clusters and markers in clusters
difMarkerPlots2

Plot dot plots of features where one cluster is significantly different from the reference cluster without processing data before hand
processforanova

Processes cluster signaling data in form for statistical analysis
findclust

Filters list to contain only desired clusters
citrus.foldFeatureSet

Correlation data for example of Citrus data set from nolanlab/citrus
sortmat

Reorders to rows (corresponding to different clusters) of a matrix of medians to a desired order
plotdif

Plot dot plots of features where both clusters are significantly different from the reference cluster