Remove specific features (CNA, repeats)

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)
#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
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)
#> ChromSCape::exclude_features_scExp - Removed 4 regions from the analysis.
scExp
#> class: SingleCellExperiment 
#> dim: 596 300 
#> metadata(0):
#> assays(1): counts
#> rownames(596): chr1_1_5147117 chr1_5147118_10294233 ...
#>   chrX_89737519_94884635 chrX_94884636_100031751
#> rowData names(1): ID
#> colnames(300): sample_1_c1 sample_1_c2 ... sample_4_c77 sample_4_c78
#> colData names(5): barcode cell_id sample_id batch_id total_counts
#> reducedDimNames(0):
#> mainExpName: main
#> altExpNames(0):