mm10.50kbp.SR50: Mm10 50kbp bin annotations

Description Value Author(s) References Examples

Description

Bin annotations are caclulated for non overlapping 50kbp bins generated as described in Scheinin et al. (see references). The annotated data frame contains:

Value

Returns an AnnotatedDataFrame object.

Author(s)

Daoud Sie

References

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Scheinin I, Sie D, Bengtsson H, van de Wiel M, Olshen A, van Thuijl H, van Essen H, Eijk P, Rustenburg F, Meijer G, Reijneveld J, Wesseling P, Pinkel D, Albertson D, Ylstra B 2014 Genome Research vol: 24 (12) pp: 1–11

Fast Computation and Applications of Genome Mappability. Derrien T, Estelle J, Sola S, Knowles D, Raineri E, Guigo R, Ribeca P January 19, 2012 PLOS ONE doi: 10.1371/journal.pone.0030377

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Gnerre S, Maccallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander E, Jaffe D 2011 Proceedings of the National Academy of Sciences of the United States of America vol: 108 no. 4 1512–1518 doi: 10.1073/pnas.1017351108

Examples

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data("mm10.50kbp.SR50")
assign("bins", get("mm10.50kbp.SR50"))
## Not run: readCounts <- binReadCounts(bins=bins, path="./bam")

# or

bins <- getBinAnnotations(binSize=50, genome="mm10")
## Not run: readCounts <- binReadCounts(bins=bins, path="./bam")

tgac-vumc/QDNAseq.mm10 documentation built on May 31, 2019, 9 a.m.