run_scaffold_analysis: High level wrapper for performing a Scaffold analysis

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

Description

This function represent a high-level entry-point for performing a Scaffold analysis

Usage

run_scaffold_analysis(
  files.list,
  ref.file,
  landmarks.data,
  col.names,
  out.dir = "scaffold_result",
  process.clusters.data = TRUE,
  downsample.to = 1000,
  ...
)

Arguments

files.list	Character vector. The list of files to process
ref.file	The name of the file to be used as reference (i.e. the first file to be processed, which will determine the position of the landmarks in all subsequent maps)
landmarks.data	The landmarks data as returned by load_landmarks or load_landmarks_from_dir
col.names	A character vector of column (i.e. marker) names to be used for the analysis. These columns have to be present in all the files
out.dir	The name of the output directory
process.clusters.data	If this is TRUE this function will look for a file with extension .all_events.rds for each file in files.list (see the Documentation of grappolo::cluster_fcs_files). This file contains single-cell data (i.e. each row represent a cell, as opposed to the files in files.list where each row represents a cluster). Each file will be processed using the write_clusters_data function. This processing is used for downstream data visualization but it is not strictly necessary to create the graph.
downsample.to	The number of events to target for downsampling when processing the clusters data. This is only used if process.cluster.data == TRUE and it does not affect the computation as this data is only used for downstream visualization
...	Additional parameters passed to get_scaffold_map

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