GreyList object for use in examples.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 Samtools.
The chromosome 21-only karyotype file was created by deleting all lines
except chromosome 21, in a file generated by fetchChromSizes as
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:
GreyList on karyotype file karyotype_chr21.txt
tiles: 94004
files: jc899_chr21.bam
size (mean): 0.370332362145541
mu (mean): 10.2330008719269
params: reps=10, sample size=1000, p-value=0.99
threshold: 81
regions: 118
coverage: 4.45%
The fields are described in the class's documentation, but briefly, we can see:
BSgenome object),
size and mu,
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.
data(greyList)GreyList object named gl.GreyList object.