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(data)
    # data(annots)
    # data(genes)

    # infercnv_obj <- infercnv::CreateInfercnvObject(raw_counts_matrix=data,
    #                                                gene_order_file=genes,
    #                                                annotations_file=annots,
    #                                                ref_group_names=c("normal"))

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

    data(infercnv_object)

    infercnv_obj <- infercnv::apply_median_filtering(infercnv_obj)
    # plot result object

[Package infercnv version 1.0.4 Index]