processSnp: process an individual SNP

In andrewGhazi/mpradesigntools: tools for designing MPRA experiments

Description

Take one SNP, get its genomic context, concatenate the parts, and check it doesn't contain aberrant digestion sites. If it does, resample the barcodes and try a few more times. If it still does, return a failure stating why.

Usage

processSnp(
  snp,
  nper,
  upstreamContextRange,
  downstreamContextRange,
  fwprimer,
  revprimer,
  enzyme1,
  enzyme2,
  enzyme3,
  alter_aberrant = FALSE,
  extra_elements = FALSE,
  max_construct_size = NULL,
  flip_RV = TRUE
)

Arguments

snp	a data_frame containing the VCF information for one SNP as well as a barcode pool to sample from.
nper	The number of barcoded sequences to be generated per allele per SNP
upstreamContextRange	the amount of sequence context to acquire upstream of the SNP
downstreamContextRange	the amount of sequence context to acquire downstream of the SNP
fwprimer	a string containing the forward PCR primer to be used
revprimer	a string containing the reverse PCR primer to be used
enzyme1	the first restriction enzyme's recognition pattern
enzyme2	the first restriction enzyme's recognition pattern
enzyme3	the first restriction enzyme's recognition pattern

Value

a data_frame of labeled sequences with appropriate information on the changes made

andrewGhazi/mpradesigntools documentation built on Dec. 21, 2020, 3:18 p.m.