tabix.read: Read tabix file, similar to running tabix in command line.

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

Read tabix file, similar to running tabix in command line.

Description

Read tabix file, similar to running tabix in command line.

Usage

tabix.read(tabixFile, tabixRange)

Arguments

tabixFile	character, an tabix indexed file
tabixRange	character, a text indicating which range in the VCF file to extract. e.g. 1:100-200

Value

character vector, each elements is an individual line

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

if (.Platform$endian == "little") {
  fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
  snp <- tabix.read(fileName, "1:196623337-196632470")
} else {
  message("Tabix does not work well for big endian for now")
}

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