Data from: The Mouse Universal Genotyping Array: from substrains to subspecies

Morgan AP, Fu C, Kao C, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F

Date Published: September 26, 2016

DOI: http://dx.doi.org/10.5061/dryad.689d2

 

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Title Genotypes matrix (markers x samples)
Downloaded 7 times
Description Genotypes matrix (markers x samples) as comma-separated values. First six headers are chromosome, marker name, genetic position (cM), physical position (bp, in build mm10/GRCm38 of the mouse reference genome), reference allele ("A1"), alternate allele ("A2"). Remaining column headers are sample names.
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Title Genotypes in PLINK binary format (*.bed; 1 of 3)
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Description Genotypes for reference samples in PLINK binary format. The PLINK format entails three separate files: *.bed (binary-encoded genotypes), *.bim (marker map) and *.fam (sample metadata).
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Title Genotypes in PLINK binary format (*.bim; 2 of 3)
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Description Genotypes for reference samples in PLINK binary format. The PLINK format entails three separate files: *.bed (binary-encoded genotypes), *.bim (marker map) and *.fam (sample metadata).
Download refsamples.bim (12.23 Mb)
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Title Genotypes in PLINK binary format (*.fam; 3 of 3)
Downloaded 3 times
Description Genotypes for reference samples in PLINK binary format. The PLINK format entails three separate files: *.bed (binary-encoded genotypes), *.bim (marker map) and *.fam (sample metadata).
Download refsamples.fam (14.50 Kb)
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Title Genotypes as a compressed R data object (*.rds)
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Description Genotypes matrix (markers x samples) as an R data object for use with the `argyle` package (https://github.com/andrewparkermorgan/argyle). The object itself is just a matrix, with marker and sample metadata as attributes. For details see the `argyle` manuscript: Morgan AP (2016) argyle: an R package for analysis of Illumina genotyping arrays. G3 6: 281-286. http://www.g3journal.org/content/6/2/281
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When using this data, please cite the original publication:

Morgan AP, Fu C, Kao C, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F (2015) The Mouse Universal Genotyping Array: from substrains to subspecies. G3: Genes - Genomes - Genetics 6(2): 263-279. http://dx.doi.org/10.1534/g3.115.022087

Additionally, please cite the Dryad data package:

Morgan AP, Fu C, Kao C, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F (2015) Data from: The Mouse Universal Genotyping Array: from substrains to subspecies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.689d2
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