PAM_spacing: PAM spacing specification
In CicciaLab/iSTOP: iSTOP - Induced STOP Experiment Design

Description Usage Arguments Details

View source: R/locate-PAM.R

Specify preferred PAM spacing when using locate_PAM.

1	PAM_spacing(optimal = c(14, 14), good = c(13, 15), ok = c(12, 16), ...)

`optimal`	defaults to `c(14, 14)`
`good`	defaults to `c(13, 15)`
`ok`	defaults to `c(12, 16)`
`...`	Additional custom named ranges can be included.

locate_PAM uses these spacing ranges to optimize PAM selection when designing guide sequences. The priority for design is optimal > good > ok > .... All arguments should be two-element numeric vectors indicating a minimum and maximum of the range. The default settings gives priority to PAMs that place the target base in the middle of the five base range of high efficiency BE3-Cas9 editing.

Note that a spacing of 14 means 14 nucleotides between the target base the first base in the PAM. For example, cNNNNNNNNNNNNNN.GG has a spacing of 14 between the targeted c and the .GG PAM pattern.

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