locate_codons: Locate codons in transcripts

In CicciaLab/iSTOP: iSTOP - Induced STOP Experiment Design

Description

Locate genome coordinates of a desired set of codons given a data.frame of CDS coordinates (see CDS), and its corresponding BSgenome sequence database.

Usage

locate_codons(
  cds,
  genome,
  codons = c("CAA", "CAG", "CGA", "TGG", "TGG"),
  positions = c(1L, 1L, 1L, 2L, 3L),
  switch_strand = c(F, F, F, T, T),
  cores = getOption("mc.cores", 1L)
)

Arguments

cds	A data.frame of CDS coordinates. See CDS for details on required columns.
genome	A BSgenome sequence database, or a Biostrings. CDS coordinates in cds should correspond to this genome assembly.
codons	A character vecor of codons to consider. Defaults to c('CAA', 'CAG', 'CGA', 'TGG', 'TGG') which are all of the codons with iSTOP targetable bases.
positions	An integer vector of positions in codons to use for returned coordinates. Should be the same length as codons. Defaults to c(1L, 1L, 1L, 2L, 3L) which are the positions in codons that can be targeted with iSTOP.
switch_strand	A logical vector indicating whether the corresponding codon is targeted on the opposite strand. Determines the resulting value of sg_strand. Should be the same length as codons. Defaults to c(F, F, F, T, T)
cores	Number of cores to use for parallel processing with pblapply

Details

Each transcript is processed independently based on the tx column of the cds data.frame.

CDS validation - Each CDS is validated by checking that the coordinates result in a DNA sequence that begins with a start codon, ends with a stop codon, has a length that is a multiple of 3 and has no internal in-frame stop codons.

No match? - If a CDS passes validation, but does not have any of the considered codons, the transcript will still be included in the resulting data.frame, but coordinates will be missing (i.e. NA).

Value

A data.frame with the following columns where each row represents a single targetable coordinate (codons with multiple targetable coordinates will have a separate row for each):

• COLUMN-NAME DATA-TYPE DESCRIPTION

• tx chr Transcript symbol

• gene chr Gene symbol

• exon int Exon rank in gene

• pep_length int Lenth of peptide

• cds_length int Length of CDS DNA

• chr chr Chromosome

• strand chr Strand (+/-)

• sg_strand chr Guide strand (+/-)

• aa_target chr One letter code of targeted amino acid

• codon chr Three letter codon

• aa_coord int Coordinate of targeted amino acid (start == 1)

• cds_coord int Coordinate of targeted base in CDS (start == 1)

• genome_coord int Coordinate of targeted base in genome

• NMD_pred lgl Is nonsense-mediated-decay predicted (i.e. target base is >56 bases upstream of last exon junction)

• rel_position dbl Relative position in CDS of the targeted base

CicciaLab/iSTOP documentation built on May 9, 2021, 4:55 p.m.