In RGLab/cytoCore: R bindings for cytolib c++ library

cytoCore

R bindings of the Core cytometry infrastructure

Installation

devtools::install_github("RGLab/RProtoBufLib", ref = "cytoset")
devtools::install_github("RGLab/cytolib", ref = "cytoset")
devtools::install_github("RGLab/cytoCore")

CytoFrame

library(cytoCore)
files <- list.files(pattern = ".fcs", "../flowWorkspace/wsTestSuite/curlyQuad/example1/", full.names = T)
fr <- load_cytoframe_from_fcs(files[1])
fr
#accessors
dim(fr)
colnames(fr)
#fetch data
head(exprs(fr))

Read header only

fr1 <- load_cytoframe_from_fcs(files[1], text.only = T)
nrow(fr1)
spillover(fr1)
#keyword
head(keyword(fr1))

Parallel read

fr <- load_cytoframe_from_fcs(files[3], num_threads = 3)

Pass by reference

fr1 <- fr #fr1 is a reference
colnames(fr1)[1]
colnames(fr1)[1] <- "t"
colnames(fr)[1] # change affects the original fr object

Shallow copy

fr1 <- fr[1:10, 2:3] #subsetting is cheap since it is merely a view of orignal fr
#they both share the same underlying data pointer
# exprs(fr1)[2] <- 0 # data change affects the orignal fr

dim(fr1)
dim(fr)

Deep copy

fr1 <- deep_copy(fr) #fr1 is independent copy

Coerce to flowFrame

as.flowFrame(fr)

Save to h5

tmpfile <- tempfile(fileext = ".h5")
write.h5(fr, tmpfile)
library(rhdf5)
h5 <- H5Fopen(tmpfile)
h5
H5Fclose(h5)

RGLab/cytoCore documentation built on May 28, 2019, 5:36 p.m.