Harmony — harmony • rCASC

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

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

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

Examples

if (FALSE) {
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)
}