loadCoordinate: Build Coordinate object.

Description

The Coordinate object is capable of loading genomic coordinates on demand. Chromosome-specific coordinates can be called in a bracket. The coordinates can also be expanded to k-mer size equally on both flanks

Usage

loadCoordinate(
  root.path = NULL,
  single.len = NULL,
  is.strand.sensitive = TRUE,
  merge.replicates = TRUE,
  rm.dup = TRUE,
  add.col.rep = FALSE,
  is.kmer = FALSE,
  k = NA,
  ori.first.index = 1,
  load.limit = 1
)

Value

Coordinate object.

Arguments

root.path: A path to a directory containing either: (1) chromosome-separated coordinate files (multiple replicates is assumed for sub-folder) or (2) bedfile (multiple replicates is assumed for separate bedfiles).
single.len: Single case length relevant when all coordinates have the same length. This is for memory optimization. Default is NULL.
is.strand.sensitive: A boolean whether strand polarity matters. Default is TRUE.
merge.replicates: Merge coordinate from different replicates. Default is TRUE. If not merging, duplicates will give weight to the k-mer counting. If add.col.rep, merged coordinate will contain column replicate e.g. "rep1&rep2".
rm.dup: Remove duplicates in each replicate. Default is TRUE.
add.col.rep: Add column replicate to the coordinate table.
is.kmer: Is the coordinate refers to k-mer i.e. expanded case? Default is FALSE.
k: Length of k-mer relevant only when is.kmer is TRUE.
ori.first.index: Indexing format of the coordinate: 0 for zero-based (start, end) and 1 for one-based (start, end). Default is 1.
load.limit: Maximum number of coordinate data.table loaded on RAM. Default is 1.