TabixFile-methods: TabixFile Import/Export

Description Usage Arguments Value Author(s) References See Also

Description

These methods support the import and export of Rsamtools:TabixFileTabixFile objects. These are generally useful when working with tabix-indexed files that have a non-standard format (i.e., not BED nor GFF), as well as exporting an object with arbitrary columns (like a GRanges) to an indexed, tab-separated file. This relies on the tabix header, which indicates the columns in the file that correspond to the chromosome, start and end. The BED and GFF parsers handle tabix transparently.

Usage

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## S4 method for signature 'TabixFile,ANY,ANY'
import(con, format, text,
                   which = if (is.na(genome)) NULL
                           else as(seqinfoForGenome(genome), "GenomicRanges"),
                   genome = NA, header = TRUE, ...)
exportToTabix(object, con, ...)

Arguments

con

For import, a TabixFile object; for exportToTabix, a string naming the destination file.

object

The object to export. It is coerced to a data.frame, written to a tab-separated file, and indexed with tabix for efficient range-based retrieval of the data using import.

format

If any known format, like “bed” or “gff” (or one of their variants), then the appropriate parser is applied. If any other value, then the tabix header is consulted for the format. By default, this is taken from the file extension.

text

Ignored.

which

A range data structure coercible to RangesList, like a GRanges. Only the intervals in the file overlapping the given ranges are returned. The default is to use the range over the entire genome given by genome, if specified.

genome

The identifier of a genome, or NA if unknown. Typically, this is a UCSC identifier like “hg19”. An attempt will be made to derive the seqinfo on the return value using either an installed BSgenome package or UCSC, if network access is available.

header

If TRUE, then the header in the indexed file, which might include a track line, is sent to the parser. Otherwise, the initial lines are skipped, according to the skip field in the tabix index header.

...

Extra arguments to pass to the underlying import routine, which for non-standard formats is read.table or write.table.

Value

For import, a GRanges object.

For exportToTabix, a TabixFile object that is directly passable to import.

Author(s)

Michael Lawrence

References

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

See Also

scanTabix and friends


Bioconductor-mirror/rtracklayer documentation built on July 28, 2017, 5:27 a.m.