assessSnp: Assess the effect of a SNP using a Trena object

In PriceLab/TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Assess the effect of a SNP using a Trena object

Description

Assess the effect of a SNP using a Trena object

Usage

## S4 method for signature '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

## Not run: 
# 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)

## End(Not run)

PriceLab/TReNA documentation built on March 21, 2023, 1:57 p.m.