TabixInput {Rsamtools}R Documentation

Operations on ‘tabix’ (indexed, tab-delimited) files.

Description

Scan compressed, sorted, tabix-indexed, tab-delimited files.

Usage


scanTabix(file, ..., param)
## S4 method for signature 'character,RangesList'
scanTabix(file, ..., param)
## S4 method for signature 'character,RangedData'
scanTabix(file, ..., param)
## S4 method for signature 'character,GRanges'
scanTabix(file, ..., param)

Arguments

file

The character() file name(s) of the tabix file be processed, or more flexibly an instance of class TabixFile.

param

A instance of GRanges, RangedData, or RangesList provide the sequence names and regions to be parsed.

...

Additional arguments, currently ignored.

Value

scanTabix returns a list, with one element per region. Each element of the list is a character vector representing records in the region.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>.

References

http://samtools.sourceforge.net/tabix.shtml

Examples

example(TabixFile)

[Package Rsamtools version 1.6.3 Index]