exportFromSeurat: Export Seurat object to Cerebro.

In romanhaa/cerebroPrepare: Export data for visualization in Cerebro.

Description

This function allows to export a Seurat object to visualize in Cerebro.

Usage

exportFromSeurat(object, file, experiment_name, organism,
  column_sample = "sample", column_cluster = "cluster",
  column_nUMI = "nUMI", column_nGene = "nGene",
  column_cell_cycle_seurat = NULL, column_cell_cycle_cyclone = NULL,
  add_all_meta_data = TRUE)

Arguments

object	Seurat object.
file	Where to save the output.
experiment_name	Experiment name.
organism	Organism, e.g. hg (human), mm (mouse), etc.
column_sample	Column in [e-mail] that contains information about sample; defaults to 'sample'.
column_cluster	Column in [e-mail] that contains information about cluster; defaults to 'cluster'.
column_nUMI	Column in [e-mail] that contains information about number of transcripts per cell; defaults to 'nUMI'.
column_nGene	Column in [e-mail] that contains information about number of expressed genes per cell; defaults to 'nGene'.
column_cell_cycle_seurat	Optional column in [e-mail] that contains information about cell cycle phase based on Regev method (default of Seurat); defaults to NULL.
column_cell_cycle_cyclone	Optional column in [e-mail] that contains information about cell cycle phase based on Cyclone method; defaults to NULL.
add_all_meta_data	If set to TRUE, all further meta data columns will be extracted as well.

Details

Export Seurat object to Cerebro.

Value

Returns object to be saved and loaded in Cerebro.

Examples

exportFromSeurat(
  object = seurat,
  file = 'PDX_patient_A.crb',
  experiment_name = 'PDX_patient_A',
  organism = 'hg',
  column_sample = 'sample',
  column_cluster = 'cluster',
  column_nUMI = 'nUMI',
  column_nGene = 'nGene',
  column_cell_cycle_seurat = 'cell_cycle_seurat',
  column_cell_cycle_cyclone = 'cell_cycle_cyclone',
  add_all_meta_data = TRUE
)

romanhaa/cerebroPrepare documentation built on Oct. 17, 2019, 4:01 p.m.