displayVarOnGeneModel: Display Variants on Gene Model

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Display Variants on Gene Model

Description

show variants on gene model using hapSummary and gene annotations

Usage

displayVarOnGeneModel(
  hapSummary,
  gff,
  Chr,
  startPOS,
  endPOS,
  type = "pin",
  cex = 0.7,
  CDS_h = 0.05,
  fiveUTR_h = 0.02,
  threeUTR_h = 0.01,
  geneElement = geneElement,
  hap
)

Arguments

hapSummary, hap	haplotype result
gff	gff
Chr	the chromosome name. If missing, the first element in the hapSummary will be used
startPOS	If missing, will use the min position in hapSummary
endPOS	If missing, will use the max position in hapSummary
type	character. Could be "circle", "pie", "pin", "pie.stack" or "flag"
cex	a numeric control the size of circle
CDS_h, fiveUTR_h, threeUTR_h	The height of CDS 5'UTR and 3'UTR in gene model
geneElement	ploted elements, eg.: c("CDS","five_prime_UTR")

Value

No return value

Examples

data("geneHapR_test")
hapSummary <- hap_summary(hapResult)
displayVarOnGeneModel(hapSummary, gff,
                      startPOS = 4100,
                      endPOS = 8210,
                      cex = 0.75)

geneHapR documentation built on May 29, 2024, 11:59 a.m.