GetContigCumulLength: GetContigCumulLength Function (SeQual)
In AlexisHardy/DNAModAnnot: Toolbox for DNA Modifications filtering and annotation

GetContigCumulLength

R Documentation

GetContigCumulLength Function (SeQual)

Description

Return a dataframe with the length (and cumulative length) of contigs (ordered from largest to smallest contig) provided in genome assembly.

Usage

GetContigCumulLength(dnastringsetGenome)

Arguments

dnastringsetGenome

A DNAStringSet object containing the sequence for each contig.

Value

A dataframe:

contig_names: The names of each contig.
Mbp_length: The size of each contig (in Megabase pairs (Mbp)).
cumsum_Mbp_length: The cumulative size (from largest to smallest contig) for each contig (in Megabase pairs (Mbp)).

Examples

myGenome <- Biostrings::readDNAStringSet(system.file(
  package = "DNAModAnnot", "extdata",
  "ptetraurelia_mac_51_sca171819.fa"
))

myContig_cumul_len_t <- GetContigCumulLength(dnastringsetGenome = myGenome)

myContig_cumul_len_t

AlexisHardy/DNAModAnnot documentation built on Feb. 27, 2023, 12:03 a.m.