schcl: Assigning cell types

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

Assigning cell types

Description

This function execute scHCL to assign cell types from Han et al Nature 2020, 581:303-309

Usage

schcl(group = c("sudo", "docker"), file, separator)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
file	a character string indicating the folder where input data are located. The input file is the output of scannobyGtf.
separator	separator used in count file, e.g. '\t', ','

Value

return a table summarizing the the cell type association for each cluster. The table is saved in the clusters folder in a file with the name including _celltypes_freq.

Author(s)

Raffaele Calogero, raffaele [dot] calogero [at] unito [dot] it, University of Torino

Examples

## Not run: 
example to be prepared

schcl(group="docker", file=paste(getwd(),"annotated_lorenz_testSCumi_mm10.csv", sep="/"), separator=",")

## End(Not run)

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