Assess the effect of a SNP using a Trena object

Assess the effect of a SNP using a Trena object

# S4 method for Trena
assessSnp(
  obj,
  pfms,
  variant,
  shoulder,
  pwmMatchMinimumAsPercentage,
  relaxedMatchDelta = 25
)

Arguments

obj

An object of class Trena
pfms

A set of motif matrices, generally retrieved using MotifDb
variant

A variant of interest
shoulder

A distance from the TSS to use as a window
pwmMatchMinimumAsPercentage

A minimum match percentage for the motifs
relaxedMatchDelta

A numeric indicating the degree of the match (default = 25)

Value

A data frame containing the gene model

Examples

if (FALSE) {
# Create a Trena object for human, assign a variant, then assess the effects of the variant
trena <- Trena("hg38")

library(MotifDb)
jaspar.human.pfms <- as.list(query(query(MotifDb, "jaspar2016"), "sapiens"))[21:25]

variant <- "rs3875089" # chr18:26865469  T->C

tbl <- assessSnp(trena, jaspar.human.pfms, variant, shoulder = 3,
pwmMatchMinimumAsPercentage = 65)
}