MEL_markers: Focal genome map (i.e., 'focalgenome') of _Drosophila...
In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements
Description
Usage
Format
References
See Also
Description
A data set representing the D. melanogaster genome with 13,818 markers
on 12 genome segments (i.e., chromosomes and scaffolds). The genome map was
generated based on publicly available genome assemblies downloaded from
Ensemble Release 91
(http://dec2017.archive.ensembl.org)
and Ensemble Metazoa Release 37
(http://oct2017-metazoa.ensembl.org).
Orthologs were identified with OMA standalone v2.2.0 (Altenhoff et al.
2015). See the package vignette for details.
Usage
1
Format
A data frame with markers in rows and six columns that specify the
structure of the D. melanogaster focal genome map:
$marker unique ortholog ID of marker
$scaff genome segment where marker is located
$start start position of marker on genome segment
$end end position of marker on genome segment
$strand reading direction of marker
$name marker name
References
Altenhoff, A.M. et al. (2015). The OMA orthology database in 2015:
function predictions, better plant support, synteny view and other
improvements. Nucleic Acids Research, 43, D240–D249. doi:
10.1093/nar/gku1158.
See Also
computeRearrs, SIM_markers,
YAK_markers, MSSYE_PQTREE_HEUR
dorolin/rearrvisr documentation built on Aug. 6, 2020, 1:32 a.m.
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Description Usage Format References See Also
Description
A data set representing the D. melanogaster genome with 13,818 markers on 12 genome segments (i.e., chromosomes and scaffolds). The genome map was generated based on publicly available genome assemblies downloaded from Ensemble Release 91 (http://dec2017.archive.ensembl.org) and Ensemble Metazoa Release 37 (http://oct2017-metazoa.ensembl.org). Orthologs were identified with OMA standalone v2.2.0 (Altenhoff et al. 2015). See the package vignette for details.
Usage
1 |
Format
A data frame with markers in rows and six columns that specify the structure of the D. melanogaster focal genome map:
$marker | unique ortholog ID of marker |
$scaff | genome segment where marker is located |
$start | start position of marker on genome segment |
$end | end position of marker on genome segment |
$strand | reading direction of marker |
$name | marker name |
References
Altenhoff, A.M. et al. (2015). The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research, 43, D240–D249. doi: 10.1093/nar/gku1158.
See Also
computeRearrs, SIM_markers,
YAK_markers, MSSYE_PQTREE_HEUR
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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