tabix.read.table: 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.table(
  tabixFile,
  tabixRange,
  col.names = TRUE,
  stringsAsFactors = FALSE
)

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
col.names	logical, use tabix file header as result headers (default: TRUE)
stringsAsFactors	logical, store loaded data as factors (default: FALSE)

Value

data frame, each elements is an individual line

See Also

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

Examples

fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
snp <- tabix.read.table(fileName, "1:196623337-196632470")

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.