This function intersects the given variants with the genes in that region and classifies them according to "intergenic", "3UTR", "exon", "intron" or "5UTR".
data.frame, Variants as returned by get.variants{get.variants}.
mgi.file
Character, full path to the MGI feature file. On the JAX campus, this defaults to "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz".
Value
FALSEor SNPs and Indels:
data.frame: with eight columns: ID, CHR, POS, REFALSE, ALT, symbol, id, type. The first four columns are simply copied over from the SNP file. The symbol column contains the Gene Symbol. The id column contains a gene ID (MGI, Ensembl, NCBI or VEGA). The type column contains "intergenic", "3UTR", "exon", "intron" or "5UTR", depending on the location of the variant in a gene.
FALSEor SVs:
data.frame: with eight columns: ID, CHR, POS, REFALSE, ALT, symbol, id, type. The first four columns are simply copied over from the SNP file. The symbol column contains the Gene Symbol. The id column contains a gene ID (MGI, Ensembl, NCBI or VEGA). The type column contains "intergenic", "3UTR", "exon", "intron" or "5UTR", depending on the location of the variant in a gene.