harmony: Harmony

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

Harmony

Description

This function performs integration of single cell genomics datasets. Korsunsky et al. Nature Methods 16, 1289, 2019

Usage

harmony(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  meta_data,
  usePCA
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
file	a character string indicating the path of the file, with file name and extension included. The file must contain library normalized cells, log transformed counts, and scaled genes
separator	separator used in count file, e.g. '\t', ','
meta_data	file with meta_data. All path included.Check example file.
usePCA	TRUE or FALSE if Harmony has to use pca or not.

Value

stability plot for each nCluster,two files with score information for each cell for each permutation.

Author(s)

Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
harmony(group="sudo", scratch.folder="/home/lucastormreig/newDockers/harmony/scratch/", file="/home/lucastormreig/newDockers/harmony/scratch/example.csv",separator=",",meta_data="/home/lucastormreig/newDockers/harmony/scratch/example_metaData.csv",usePCA=FALSE)

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.