apply_median_filtering {infercnv} | R Documentation

## 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

[Package infercnv version 1.10.1 Index]