get2status: Filters matrix columns based on two conditions per file, e.g....

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

Description

Filters matrix columns based on two conditions per file, e.g. patient status, stimluation, time points, etc.

Usage

get2status(key1, key2, results)

Arguments

key1	- Search string of interest for names
key2	- Search string of interest for names
results	- Results matrix with fcs files corresponding to columns

Value

Returns a list of IDs with names matching search both serach strings with names being the description of these features

Examples

#Example starting with obtaining data from Cytobank
library(CytobankAPI)
cyto_session <- authenticate(site="premium", username="myusername", password="mypassword")
markersofinterest<-c("CD3","CD56")
popsofinterest<-c("CD4 T cells","NK cells")
exptID=4
type=F
results<-analyzedata(cyto_session,markersofinterest,popsofinterest,exptID,type)
key1<-"Patient"
key2<-"Untreated"
get2status(key1,key2,results)

#Example with simple data matrix
data<-matrix(1:18,nrow=3,ncol=6,byrow=TRUE)
colnames(data)<-c("Ctrl1 unst","Pt1 unst","Pt3 unst","Ctrl1 stim","Pt1 stim","Pt3 stim")
rownames(data)<-c("Marker1","Marker2","Marker3")
#Getting all stimulated patient samples
get2status(c("Pt","Ctrl"),"stim", data)
#Getting all stimulated patient and control samples
get2status(c("Pt","Ctrl"),"stim", data)

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