getNucleotideContent: Get sequence content from one or multiple FASTA sequences.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Get sequence content from one or multiple FASTA sequences.

Description

This function takes a single or set of FASTA sequences and for each sequence will report counts and frequencies of user defined ‘sequence.pattern' (such as exact DNA pattern, e.g. ’GA') or 'nucleotide.content' (such as sequence GC content).

Usage

getNucleotideContent(
  fasta.seq,
  sequence.pattern = NULL,
  nucleotide.content = NULL
)

Arguments

fasta.seq	A DNAStringSet-class object containing one or multiple FASTA sequences.
sequence.pattern	A user defined DNA sequence pattern which occurrences will be counted in submitted 'fasta.seq'. (e.g. set ‘sequence.pattern' to ’GA' to obtain counts of all 'GA' occurrences per FASTA sequence).
nucleotide.content	A user defined nucleotides which total content will be counted in submitted 'fasta.seq'. (e.g. to obtain 'GC' content set ‘nucleotide.content' to ’GC')

Author(s)

David Porubsky

Examples

## Get PAF to process ##
paf.file <- system.file("extdata", "test_getFASTA.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Get FASTA to process
asm.fasta <- system.file("extdata", "test_getFASTA_query.fasta", package = "SVbyEye")
## Read in FASTA sequence
fasta.seq <- paf2FASTA(paf.table = paf.table, asm.fasta = asm.fasta)
## Report sequence and nucleotide content for a given FASTA sequence
getNucleotideContent(fasta.seq = fasta.seq, sequence.pattern = "AT", nucleotide.content = "GC")

daewoooo/SVbyEye documentation built on March 31, 2024, 8:58 a.m.