STUDY_GENIC_ELEMENTS: Study k-mer composition across species.

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Study k-mer composition across species.

Description

Study k-mer composition across species.

Usage

STUDY_GENIC_ELEMENTS(
  kmer.table,
  kmer.cutoff = 5,
  k,
  genome.name = "hg38",
  central.pattern = NULL,
  db = "refseq",
  output.dir = "study_genic_elements/",
  fasta.path
)

Arguments

kmer.table	A data.table of kmer table.
kmer.cutoff	Percentage of extreme kmers to study. Default to 5.
k	K-mer size.
genome.name	UCSC genome name.
central.pattern	K-mer's central patterns. Default is NULL.
db	Database used by UCSC to generate gene prediction: "refseq" or "gencode". Default is "refseq".
output.dir	A directory for the outputs.
fasta.path	Path to a directory of user-provided genome FASTA files or the destination to save the NCBI/UCSC downloaded reference genome files.

Value

An output directory containing plots.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.