User: Samuel Younkin

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5 years, 5 months ago
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Posts by Samuel Younkin

<prev • 6 results • page 1 of 1 • next >
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Packages not in BioC or CRAN
... What is the Bioconductor policy on accepting packages that import packages not available at BioC or CRAN. The external package would be available at a public website instead. Assume that the licensing of the external package is appropriate. Thanks, Sam ...
written 5.4 years ago by Samuel Younkin60 • updated 5.4 years ago by Martin Morgan ♦♦ 23k
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snpStats --- MAF in Pedigrees
... BioC, I have been using snpStats to analyze case-parent sequence data, and I have found that it would be useful to have a method for the class snpMatrix (along with a pedigree object of some sort) that computed the minor allele frequency in the parents only. Does anyone know if that method exists ...
snpstats written 6.5 years ago by Samuel Younkin60 • updated 6.5 years ago by Vincent J. Carey, Jr.6.3k
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rtracklayer export method requires unique names
... BioC, It seems that the export method in rtracklayer for the GRanges class requires that the GRanges object have unique names. The error message given when names are not unique is the following: Error in export(object, FileForFormat(con), ...) : cannot export object of class 'GRanges' As one ...
rtracklayer written 6.5 years ago by Samuel Younkin60 • updated 6.5 years ago by Michael Lawrence11k
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VariantAnnotation ALT Field
... I have been looking at the VariantAnnotation vignette and have encountered something strange. The R code is below. See how the ALT field lists only ########. The vignette, however, correctly shows the alternate allele. The data file chr22.vcf.gz also correctly contains the alternate allele infor ...
variantannotation written 6.7 years ago by Samuel Younkin60 • updated 6.7 years ago by Paul Shannon750
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Comment: C: GWASTools mendelList Constructor
... Thanks Stephanie, your response was very helpful. One thing I found was that the offspring, father and mother vectors must be character vectors, not factor vectors. If they are factors mendelList() will not work. One must be careful not to let them be coerced into factors, say during construction ...
written 6.9 years ago by Samuel Younkin60
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GWASTools mendelList Constructor
... BioC, I am trying to use the Mendelian error checking feature of the Bioconductor package GWASTools. When I try to create a mendelList object using the constructor function mendelList(), it consistently returns NULL with no warning or error message. I have tried changing the subject ids to charac ...
gwastools written 6.9 years ago by Samuel Younkin60 • updated 6.9 years ago by Stephanie M. Gogarten660

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