assessSnp,Trena-method {trena} | R Documentation

## 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)

[Package trena version 1.12.1 Index]