locate_PAM: Locate PAM near a genomic coordinate

In CicciaLab/iSTOP: iSTOP - Induced STOP Experiment Design

Description

Uses the results of locate_codons to determine whether there is an available PAM with desired spacing from the genomic coordinate of the targeted base.

Usage

locate_PAM(
  codons,
  genome,
  spacing = PAM_spacing(),
  PAM = PAM_patterns_default(),
  flanking = 150,
  keep_PAM = FALSE
)

Arguments

codons	A dataframe resulting from locate_codons.
genome	A BSgenome sequence database, or a Biostrings. Used to extract the genomic sequence context for each genomic coordinate in codons.
spacing	The result of PAM_spacing, which is a named list of two-element numeric vectors. Each two-element vector defines a range of spacing between an edited base and the PAM (i.e. the minimum and maximum allowable nucleotides between the targeted base and the PAM). Each pair of ranges is checked in order with the first range prioritized over the next. Defaults to PAM_spacing().
PAM	A named list of PAM patterns to be considered (see PAM_pattern). Names correspond to resulting column names in the returned dataframe. Default PAM patterns include .GG, .GA, .GCG, .GAG, ..G[AG][AG]T, and ...[AG][AG]T.
flanking	An number specifying how much flanking genomic context to return in the resulting dataframe. Defaults to 150.
keep_PAM	Logical. Should the PAM sequence be included in the guides? Defaults to FALSE.

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