cytoBatchNorm

The goal of cytoBatchNorm is to normalize cytometry data using a control sample that is labeled and measured in each batch.

Installation

cytoBatchNorm is not available on CRAN.

Simplest way to install

# Install BiocConductor manager if not already done
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
# Install cytoBatchNorm
BiocManager::install(c("i-cyto/cytoBatchNorm"))

Alternative installation

First, be sure to install flowCore from Bioconductor.

# Only once per R and BiocConductor installation
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (!require("flowCore", quietly = TRUE)) BiocManager::install(c("flowCore"))

Then, you can install the latest version of cytoBatchNorm from GitHub with:

# the devtools package must be present
# if not, install devtools with the following command
# install.packages("devtools")
devtools::install_github("i-cyto/cytoBatchNorm")

Usages

Graphical User Interface

For an interactive use, type the following commands:

# load the library, once per R session
library(cytoBatchNorm)
# execute the following command for each dataset or set of parameters
cytoBatchNormGUI(roots = c(PRJ="/path/to/results", FCS="/path/to/FCS_files"))
# you have to set the paths to results and FCS files
# if you don't know how to retrieve these 2 information, then for each path,
# use the command to select any file in the target path:
# gsub("\\", "/", dirname(file.choose()), fixed = TRUE)

Writing scripts

For using the API, look at vignettes.