Computes Signaling and Population Stats for Cytometry Data on Cytobank using 'CytobankAPI'


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Documentation for package ‘CytobankAPIstats’ version 2.0

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analyzedata Returns a matrix of event counts or raw medians, as specified by inputs. Columns correspond to fcs files and rows to markers in cell types
asinnorm Computes the arcsinh ratio of a matrix in relation to the specified column
calcperevent Calculates percentages of of cell types of interest out of total cell population
CytobankAPIstatsGUI Exports processed events and signaling data
filterfiles Filters a list of fcs files by search terms
get1status Filters matrix based on single sample name condition
get2status Filters matrix columns based on two conditions per file, e.g. patient status, stimluation, time points, etc.
getfcsfiles Gets fcs ID numbers and sample names from a given experiment
getmarkers Gets appropriate marker IDs for channels of interest
getnewind Rearranges signaling results matrix with rows in the desired order as outputs
getpops Gets appropriate gate set IDs for populations of interest
getrawsignals Computes the untransformed medians for cellular markers in populations of interest
parseevents Modifies the list obtained from a call to statistics.events to a matrix with rows corresponding to fcs files and columns corresponding to the population types
parsestats Takes the results of a call to statistics.general and returns a matrix of raw medians with columns corresponding to fcs files and rows to molecules of interest in different cell types
parsestatsmean Takes the results of a call to statistics.general and returns a matrix of raw means with columns corresponding to fcs files and rows to molecules of interest in different cell types
percentevent Calculates the percentage of cell populations given an experiment