Assigning cell types

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

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

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

Examples