Ivan,
The RangedData class can store strand information in its values table.
The values table can store any "vector-like" object from simple R
vectors (including lists) to an instance of any of the *List classes
defined in IRanges. If you use rtracklayer's import function on a bed
file containing the information you have shown, the chromosome
information will be used to segment the other values into spaces, the
start and end values will be joined together in the ranges information
(as a CompressedIRangesList object) and the strand information will be
stored as a factor column across the values set (which is a
CompressedDataFrameList object). The strand information can be accessed
by the strand accessor function. If your data are sorted by strand
within chromosome, you could add another level of compression by storing
the strand information as a 'factor' Rle in the values table instead of
a plain factor. rtracklayer's export function is aware of a possible
strand column in the values table and handles it appropriately when
serializing a RangedData object back into a bed file.
Patrick
Ivan Gregoretti wrote:
Hi everybody,
What is the minimal container class for position-and-orientation of
Solexa reads?
For example, the minimal positional information should be something
like a BED record, like this
chr1\t3000001\t3000036\t\t\t+\t
...(and many more lines)...
sorry for the cumbersome string but I just want to stress that the
minimal information is:
column 1: chromosome
column 2: start
column 3: end
column 6: orientation, either 'plus', 'minus' or undefined. (in this case a '+')
Is there any compact container to load, say, 50 million records? I
thought that RangedData could do that but after reading the
documentation I see that it does not hold strand information.
If there is such container, how do you load it up from a BED file?
Thank you,
Ivan
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
