plotMB: Plot a genomic region surrounding a genomic variant, and...

In Simon-Coetzee/motifBreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

Plot a genomic region surrounding a genomic variant, and potentially disrupted motifs

Description

Plot a genomic region surrounding a genomic variant, and potentially disrupted motifs

Usage

plotMB(
  results,
  rsid,
  reverseMotif = TRUE,
  effect = c("strong", "weak"),
  altAllele = NULL
)

Arguments

results	The output of motifbreakR
rsid	Character; the identifier of the variant to be visualized
reverseMotif	Logical; if the motif is on the "-" strand show the the motifs as reversed FALSE or reverse complement TRUE
effect	Character; show motifs that are strongly effected c("strong"), weakly effected c("weak"), or both c("strong", "weak")
altAllele	Character; The default value of NULL uses the first (or only) alternative allele for the SNP to be plotted.

Details

plotMB produces output showing the location of the SNP on the chromosome, the surrounding sequence of the + strand, the footprint of any motif that is disrupted by the SNP or SNV, and the DNA sequence motif(s). The altAllele argument is included for variants like rs1006140 where multiple alternate alleles exist, the reference allele is A, and the alternate can be G,T, or C. plotMB only plots one alternate allele at a time.

Value

plots a figure representing the results of motifbreakR at the location of a single SNP, returns invisible NULL.

See Also

See motifbreakR for the function that produces output to be visualized here, also snps.from.rsid and snps.from.file for information about how to generate the input to motifbreakR function.

Examples

data(example.results)
example.results

library(BSgenome.Hsapiens.UCSC.hg19)
plotMB(results = example.results, rsid = "rs1006140", effect = "strong", altAllele = "C")

Simon-Coetzee/motifBreakR documentation built on April 28, 2024, 2:31 a.m.