loadCoordinate: Build Coordinate object.
In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

loadCoordinate

R Documentation

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
)

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.