PAM_pattern: PAM patterns

Description Usage Arguments

View source: R/locate-PAM.R

Description

Specify PAM patterns for use with locate_PAM

Usage

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PAM_pattern(pattern, width)

PAM_patterns_default(
  sgNGG = PAM_pattern(".GG", 3),
  sgNGA = PAM_pattern(".GA", 3),
  sgNGCG = PAM_pattern(".GCG", 4),
  sgNGAG = PAM_pattern(".GAG", 4),
  sgNNGRRT = PAM_pattern("..G[AG][AG]T", 6),
  sgNNNRRT = PAM_pattern("...[AG][AG]T", 6),
  ...
)

Arguments

pattern

A regular expression used to identify a PAM. See the regex documentation for extensive help on regular expressions.

width

A single number indicating the expected width of the PAM sequence.

sgNGG

Pattern for NGG. Defaults to PAM_pattern(".GG", 3)

sgNGA

Pattern for NGA. Defaults to PAM_pattern(".GA", 3)

sgNGCG

Pattern for NGCG. Defaults to PAM_pattern(".GCG", 4)

sgNGAG

Pattern for NGAG. Defaults to PAM_pattern('.GAG', 4)

sgNNGRRT

Pattern for NNGRRT. Defaults to PAM_pattern('..G[AG][AG]T', 6)

sgNNNRRT

Pattern for NNNRRT. Defaults to PAM_pattern('...[AG][AG]T', 6)

...

Additional PAM patterns to include in PAM_patterns_default()


EricEdwardBryant/iSTOP documentation built on May 9, 2021, 6:59 p.m.