Convert gef to Giotto — gefToGiotto • GiottoClass

Converts .gef file (output stereo-seq pipeline) into giotto subcellular object

Usage

gefToGiotto(
  gef_file,
  bin_size = "bin100",
  gene_column = NULL,
  verbose = FALSE,
  h5_file = NULL
)

gef_file: path to .gef file
bin_size: bin size to select from .gef file
gene_column: (optional) character. Which column contains gene names within the geneExp information.
verbose: be verbose
h5_file: name to create and on-disk HDF5 file

giotto object

Function in beta. Converts .gef object to Giotto object.

There are six possible choices for bin_size: bin1, bin10, bin20, bin50, bin100, bin200.

See SAW pipeline for additional information about the gef file.