Rsamtools:TabixFile{TabixFile} 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.## S3 method for class 'TabixFile,character,ANY':
import(con, format, text,
which = if (is.na(genome)) NULL
else as(seqinfoForGenome(genome), "GenomicRanges"),
genome = NA, header = TRUE, ...)
## S3 method for class 'TabixFile,missing,ANY':
import(con, format, text, ...)
exportToTabix(object, con, ...)import, a TabixFile object;
for exportToTabix, a string naming the destination file.data.frame, written to a tab-separated file, and indexed with
tabix for efficient range-based retrieval of the data using
import.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.NA if
unknown. Typically, this is a UCSC identifier like seqinfo on the return
value using either an installed BSgenome package or UCSC, if network
access is available.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.read.table or
write.table.import, a GRanges object. For exportToTabix, a TabixFile object that is directly
passable to import.
scanTabix and friends