The mapsnp package leverages the Gviz system 7] to plot a genomic map for SNPs. A SNP map includes five tracks, an ideogram track
for a chromosome, an axis track for genomic coordinates, a transcript track for relevant
transcripts, a SNP location track, and a SNP label track annotating their ID symbol.
The mapsnp v0.2 package contains one function, ‘msb’. The function has three mandate
parameters, ‘M’, ‘start’, and ‘end’. Parameter ‘M’ is a data frame consist of three
columns, including chromosome, SNP ID, and SNP genomic location. The ‘start’ and ‘end’
parameter define the range of a highlighting region, typically a gene region where
the SNPs are located to. For transcript track, the ‘msb’ function utilizes Homo Sapiens
data from UCSC build hg19 based on the knownGene table, implemented in the ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
package 9].
There are dozens of other parameters, which fine-tune other track properties, such
as color, size, track name, annotation text, and so on. The detailed usage of the
package is described in Additional file 1.