apply_median_filtering: apply_median_filtering

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

apply_median_filtering

Description

Apply a median filtering to the expression matrix within each tumor bounds

Usage

apply_median_filtering(
  infercnv_obj,
  window_size = 7,
  on_observations = TRUE,
  on_references = TRUE
)

Arguments

infercnv_obj	infercnv_object
window_size	Size of the window side centered on the data point to filter (default = 7).
on_observations	boolean (default=TRUE), run on observations data (tumor cells).
on_references	boolean (default=TRUE), run on references (normal cells).

Value

infercnv_obj with median filtering applied to observations

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::apply_median_filtering(infercnv_object_example)
# plot result object

broadinstitute/infercnv documentation built on Feb. 2, 2025, 11:16 p.m.