exclude_features_scExp {ChromSCape} | R Documentation |
Remove specific features (CNA, repeats)
exclude_features_scExp( scExp, features_to_exclude, by = "region", verbose = TRUE )
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) |
A SingleCellExperiment object without features to exclude.
raw <- create_scDataset_raw() scExp = create_scExp(raw$mat, raw$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