Operations on ‘tabix’ (indexed, tab-delimited) files.
Scan compressed, sorted, tabix-indexed, tab-delimited files.
scanTabix(file, ..., param) ## S4 method for signature 'character,IntegerRangesList' scanTabix(file, ..., param) ## S4 method for signature 'character,GRanges' scanTabix(file, ..., param)
file |
The character() file name(s) of the tabix file be
processed, or more flexibly an instance of class
|
param |
A instance of |
... |
Additional arguments, currently ignored. |
scanTabix returns a list, with one element per region. Each element
of the list is a character vector representing records in the region.
scanTabix signals errors using signalCondition. The
following errors are signaled:
scanTabix_paramyieldSize(file) must be NA when
more than one range is specified.
scanTabix_ioA read error occured while inputing the
tabix file. This might be because the file is corrupt, or of
incorrect format (e.g., when path points to a plain text
file but index is present, implying that path should
be a bgziped file. The error message may include an error
code representing the logical OR of these cryptic signals: 1,
BGZF_ERR_ZLIB; 2, BGZF_ERR_HEADER; 4, BGZF_ERR_IO; 8,
BGZF_ERR_MISUSE.
Martin Morgan <mtmorgan@fhcrc.org>.
example(TabixFile)
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