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

Description Usage Arguments Value See Also Examples

View source: R/seqminer.R

Description

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

Usage

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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

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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 Aug. 4, 2018, 5:05 p.m.