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assessSnp.Rd
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assessSnp.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Trena.R
\name{assessSnp,Trena-method}
\alias{assessSnp,Trena-method}
\alias{assessSnp}
\title{Assess the effect of a SNP using a Trena object}
\usage{
\S4method{assessSnp}{Trena}(
obj,
pfms,
variant,
shoulder,
pwmMatchMinimumAsPercentage,
relaxedMatchDelta = 25
)
}
\arguments{
\item{obj}{An object of class Trena}
\item{pfms}{A set of motif matrices, generally retrieved using MotifDb}
\item{variant}{A variant of interest}
\item{shoulder}{A distance from the TSS to use as a window}
\item{pwmMatchMinimumAsPercentage}{A minimum match percentage for the motifs}
\item{relaxedMatchDelta}{A numeric indicating the degree of the match (default = 25)}
}
\value{
A data frame containing the gene model
}
\description{
Assess the effect of a SNP using a Trena object
}
\examples{
\dontrun{
# 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)
}
}