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,IntegerRangesList'
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
|
param |
A instance of |
... |
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. If
param
is empty then all records will be returned.
Error
scanTabix
signals errors using signalCondition
. The
following errors are signaled:
scanTabix_param
yieldSize(file)
must be NA when more than one range is specified.scanTabix_io
A 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 butindex
is present, implying thatpath
should be abgzip
ed 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.
Author(s)
Martin Morgan <mtmorgan@fhcrc.org>.
References
http://samtools.sourceforge.net/tabix.shtml
Examples
example(TabixFile)