Usage
variant.plot( var.file = "http://cgd.jax.org/tools/SNPtools/Build38/sanger.snps.NCBI38.txt.gz", mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz", chr, start, end, type = c("snp", "indel", "sv"), strains = c("A/J", "C57BL/6J", "129S1/SvImJ", "CAST/EiJ", "NOD/ShiLtJ", "NZO/HlLtJ", "PWK/PhJ", "WSB/EiJ"), ref = "C57BL/6J", pattern, qtl)
Arguments
var.file
Character string with the full path to the tabix indexed Sanger/UNC SNP file. Default is a file at the Center for Genome Dynmaics at the Jackson Laboratory.
mgi.file
Character string with the full path to the tabix indexed MGI feature file. Default is a file at the Center for Genome Dynmaics at the Jackson Laboratory.
chr
Character with the chromosome ID to plot on. Required.
start
Numeric value with the start position to plot at. May be in bp or Mb. If the value is 200 or less, it is assumed to be in Mb. Otherwise it is assumed to be in bp. Required.
end
Numeric value with the end position to plot at. May be in bp or Mb. If the value is 200 or less, it is assumed to be in Mb. Otherwise it is assumed to be in bp. Required.
type
Character indicating the type of variant to retrieve. One of "snp", "indel", or "sv". Default = "snp".
strains
Character vector with the strains to use. Must be from the set of strains returned by get.strains{get.strains}
. Default = Collaborative Cross/Diversity Outbred founders.
ref
Character string with the reference strain. Must be one of the names in the strains vector argument. Default = C57BL/6J.
pattern
Character vector with strain names in the strains argument. We search for SNPs for which these strains have one allele and all other strains have the opposite allele. A more sophisticated pattern matching method may be included in future releases. Default = NULL.
qtl
data.frame with QTL values containing the chromosome, bp position and QTL score in column 1 to 3. Default = NULL.