parsestats: Takes the results of a call to statistics.general and returns...

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

Description

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

Usage

parsestats(results, popsinterest, fcs, markersofinterest)

Arguments

results	- The results of a call to statistics.general function
popsinterest	- List of gateSetID numbers for populations of interest with descriptions as name
fcs	- List of fcs file IDs of interest with description of FCS file names as names
markersofinterest	- List of ID numbers for markers of interest with descriptions as name

Value

Returns a matrix of median signaling intensities with columns corresponding to fcs files and rows corresponding to markers of interest in cell types of interest

Examples

library(CytobankAPI)

cyto_session <- authenticate(site="premium", username="myusername", password="mypassword")
exptno<-2
popsofinterest1<-c("CD4 T cells","NK cells")
popsinterest<-getpops(popsofinterest1,exptno,cyto_session)
fcs<-getfcsfiles(exptno,cyto_session)
markersofinterest1<-c("CD3","CD56")
markersofinterest<-getmarkers(markersofinterest1,exptno,cyto_session)
results<-statistics.general(UserSession=cyto_session, experiment_id=2, gate_version = -1, 
compensation_id=1,fcs_files=fcs, populations = popsinterest,
output = "default",timeout = UserSession@long_timeout)
parsestats(results,popsinterest,fcs,markersofinterest)

CytobankAPIstats documentation built on May 2, 2019, 8:27 a.m.