load_landmarks: Load landmark populations from a list of FCS files

In ParkerICI/scgraphs: Analyzing single-cell data using graphs

Description

Load landmark populations from a list of FCS files

Usage

load_landmarks(files.list, asinh.cofactor, transform.data, ...)

Arguments

files.list	The list of files to load. The population names will be derived by splitting the file name using "_" as separator, and taking the last field
asinh.cofactor	The cofactor to use for asinh transformation. If this is NULL no transformation is applied
...	Additional arguments passed to flowCore::read.FCS

Value

Returns a list with the following elements:

• landmarks.data: a data.frame containing the entirety of the data

• tab.landmarks: a data.frame with the data for the landmark nodes. Each row is a separate landmark population, and the columns correspond to the median expression values of each marker. The data.frame also contains a column called cellType which contains the name of the corresponding landmark. In order to derive the name of the landmark. the name of the corresponding FCS file is split on the "_" character, and the last field is used for the landmark name.

ParkerICI/scgraphs documentation built on April 30, 2021, 1:10 p.m.