count_features: Count Features
In rpolicastro/ZentTools: What the Package Does (One Line, Title Case)

Count Features

count_features(
  zent_obj,
  outdir = getwd(),
  count_feature = "exon",
  aggregate_feature = "gene_id",
  multiple_overlap = FALSE,
  minimum_overlap = 10,
  largest_overlap = TRUE,
  read_extension_3prime = 0,
  multi_mapping = FALSE,
  multi_mapping_frac = FALSE,
  strand_specific = 0
)

`zent_obj`	Zent object.
`outdir`	Output directory for counts.
`count_feature`	Reads will be counted against this genomic feature type, such as the default 'exon' (GTF.featureType).
`aggregate_feature`	Features such as 'exons' will have their counts aggregated based on this feature type, such as the default 'gene_id' (GTF.attrType).
`multiple_overlap`	Whether to allow reads to overlap with more than one feature.
`minimum_overlap`	The minimum number of bases that the read needs to overlap to be counted.
`largest_overlap`	Whether the read will be assigned to the feature it has the most overlapping bases with.
`read_extension_3prime`	The number of bases to extend the read downstream from the 3' end.
`multi_mapping`	Whether to count multi-mapping reads.
`multi_mapping_frac`	Whether multi-mapping reads are counted as fractions.
`strand_specific`	Either 0 (unstranded), 1 (stranded), or 2 (reverse stranded).