This is a sample
GreyList object, covering
only human chromosome 21 (from genome version hg19). The input library
used to generate this grey list can be found in the European Nucleotide
Archive, under accession number ERR336953.
The library was made from a culture of the MCF-7 cell line, bought from ATCC.
The library was sequenced to a depth of 35,716,191 reads on an Illumina
Genome Analyzer IIx. The reads were aligned to human reference genome hg19
(GRCh37) using BWA version 0.7.5a with default parameters. Approximately
96% of reads aligned to the reference genome.
Reads aligning to chromosome 21 were extracted using
The chromosome 21-only karyotype file was created by deleting all lines
except chromosome 21, in a file generated by
described in the vignette. This package was then used to create the
GreyList sample object.
When printed, the object displays several important slots in the object (if they have been filled with calculated values). For example, this object has all its slots filled, indicating that the analysis is complete:
1 2 3 4 5 6 7 8 9
The fields are described in the class's documentation, but briefly, we can see:
the name of the karyotype file (or
the number of tiles (overlapping by 1/2 the tile width),
the BAM file(s) used for read counting (currently only 1 is allowed),
the two estimated parameters of the negative binomial distribution,
the input parameters,
the calculated read depth cutoff (over 1kb tiles),
the number of distinct regions, and
the percentage coverage of the reference genome.
The fact that all the fields are present indicates that the regions have been generated; otherwise fields still without values would be omitted. Of course any stage can be re-run with different parameters.
GreyList object named