exclude_features_scExp {ChromSCape} | R Documentation

## Remove specific features (CNA, repeats)

### Description

Remove specific features (CNA, repeats)

### Usage

    exclude_features_scExp(
      scExp,
      features_to_exclude,
      by = "region",
      verbose = TRUE
    )

### Arguments

`scExp` | A SingleCellExperiment object.
`features_to_exclude` | A GenomicRanges object or data.frame containing genomic regions or features to exclude or path towards a BED file containing the features to exclude.
`by` | Type of features. Either 'region' or 'feature_name'. If 'region', will look for genomic coordinates in columns 1-3 (chr,start,stop). If 'feature_name', will look for a genes in first column. ('region')
`verbose` | (TRUE)

### Value

A SingleCellExperiment object without features to exclude.

### Examples

    scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)
    features_to_exclude = data.frame(chr=c("chr4","chr7","chr17"),
    start=c(50000,8000000,2000000),
    end=c(100000,16000000,2500000))
    features_to_exclude = as(features_to_exclude,"GRanges")
    scExp = exclude_features_scExp(scExp,features_to_exclude)
    scExp

[Package ChromSCape version 1.2.62 Index]