annotateGene: Annotate a test variant

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Annotate a test variant

Description

Annotate a test variant

Usage

annotateGene(param, chrom, position, ref, alt)

Arguments

param	a list of annotation configuaration (e.g. reference file, gene definition)
chrom	a vector of chromosome names
position	a vector of chromosome positions
ref	a vector of reference alleles
alt	a vector of alternative alleles

Value

annotated results in a data frame structure

See Also

makeAnnotationParameter

Examples

if (.Platform$endian == "little") {
  param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
                geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
  param <- makeAnnotationParameter(param)
  print(param)
  annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
} else {
  message("Tabix does not work well for big endian for now")
}

seqminer documentation built on Sept. 2, 2023, 9:08 a.m.