sample_object: sample_object

In broadinstitute/inferCNV: Infer Copy Number Variation from Single-Cell RNA-Seq Data

sample_object

Description

Apply sampling on an infercnv object to reduce the number of cells in it and allow faster plotting or have all groups take up the same height on the heatmap

Usage

sample_object(
  infercnv_obj,
  n_cells = 100,
  every_n = NULL,
  above_m = NULL,
  on_references = TRUE,
  on_observations = TRUE
)

Arguments

infercnv_obj	infercnv_object
n_cells	Number of cells that should be sampled per group (default = 100).
every_n	Sample 1 cell every_n cells for each group. If subclusters are defined, this will make sure that at least one cell per subcluster is sampled. Requires above_m to be set to work, overriding n_cells parameter.
above_m	Sample groups that have at least above_m cells. Requires every_n to be set to work, overriding n_cells parameter
on_references	boolean (default=TRUE), sample references (normal cells).
on_observations	boolean (default=TRUE), sample observations data (tumor cells).

Value

sampled infercnv_obj

Examples

# data(infercnv_data_example)
# data(infercnv_annots_example)
# data(infercnv_genes_example)

# infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, 
#                                                           gene_order_file=infercnv_genes_example,
#                                                           annotations_file=infercnv_annots_example,
#                                                           ref_group_names=c("normal"))

# infercnv_object_example <- infercnv::run(infercnv_object_example,
#                                          cutoff=1,
#                                          out_dir=tempfile(), 
#                                          cluster_by_groups=TRUE, 
#                                          denoise=TRUE,
#                                          HMM=FALSE,
#                                          num_threads=2,
#                                          no_plot=TRUE)

data(infercnv_object_example)

infercnv_object_example <- infercnv::sample_object(infercnv_object_example, n_cells=5)
# plot result object

broadinstitute/inferCNV documentation built on Nov. 21, 2024, 12:06 a.m.