The inter-mutational distance (IMD) is the distance between each somatic substitution and the substitution immediately prior (Nik-Zainal et al. 2012). The imd() is used to graph the rainfall plot (Nik-Zainal et al. 2012). This graph localizes the regional clustering of mutations and represents the IMD on the y-axis on a log base 10 scale, with mutations ranked and ordered on the x-axis from the first variant on the short arm of chromosome 1 to the last variant on the long arm of chromosome X.
Several features were observed in the hyper-mutated zones, for example, kataegis is the proposed name for the hyper-mutated zones with a cluster of C>T and/or C>G mutations that are substantially enriched at TpCpN trinucleotides, on the same DNA strand and that co-localize with large-scale genomic structural variation (Alexandrov et al. 2013; Nik-Zainal et al. 2012).
● Data Source:
CranContrib
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● Alias: features
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showers() identifies all groups of closely spaced mutations using the anti-Robinson matrix. Hyper-mutated regions are defined as those segments containing a number (min = 6) or more mutations with a distance that is less than or equal to a number (max=1000) of bp, and referred to as mutation showers (Drake 2007a; Wang et al. 2007), clustered mutations (Drake 2007a; Drake 2007b; Roberts et al. 2012), or kataegis (from the Greek word for shower or thunderstorm) (Alexandrov et al. 2013; Nik-Zainal et al. 2012). showers() can be used to locate complex mutations (Roberts et al. 2012; Roberts et al. 2013) (min = 2; max=10).
This function computes and returns the Euclidean distance matrix, where each cell represents the distance in base pairs between the chromosomal position of somatic mutations. The matrix can be used to graph the anti-Robinson matrix using the seriation technique (Hahsler and Hornik 2011). Plotting the distance matrix helps to visualize and identify mutation clusters in addition to locating the micro-clustered mutated regions within the macro-clustered mutated zones that occur during the oncogenic process.
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