showers {ClusteredMutations}R Documentation

Location of clustered mutations in the cancer genome.


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).


showers(data = NULL, chr = NULL, position, min = 6, max = 5000)



: somatic substitution mutations of the cancer genome data set.


: chromosome where the somatic mutation is located.


: position of somatic mutations in the DNA sequence of the cancer genome.


: a number min of consecutive mutations.


: a distance less than or equal to a number max of bp.


By default, showers() identifies the hyper-mutated zones (min = 6; max=5000). Complex mutations are those segments containing >= 2 consecutive mutations with a distance =< 100 bp.


showers() returns a data set with all hyper-mutated zones in the DNA sequence of tumor cells.


: the shower mutations data set contains seven variables: chromosome.


: the last position in the chromosome of the mutation shower.


: the first position in the chromosome of the mutation shower.


: the last number of a consecutive mutation shower.


: the first number of a consecutive mutation shower.


: the length of a hyper-mutated zone and the number of mutations in the clustered mutation.


David Lora.


Alexandrov LB, Nik-Zainal S, Wedge DC, et al. Signatures of mutational processes in human cancer. Nature. 2013 Aug 22;500(7463):415-21.

Drake JW. Mutations in clusters and showers. Proc Natl Acad Sci U S A. 2007 May 15;104(20):8203-4.

Drake JW. Too many mutants with multiple mutations. Crit Rev Biochem Mol Biol. 2007 Jul-Aug;42(4):247-58.

Nik-Zainal S, Alexandrov LB, Wedge DC, et al; Breast Cancer Working Group of the International Cancer Genome Consortium. Mutational processes molding the genomes of 21 breast cancers. Cell. 2012 May 25;149(5):979-93.

Roberts SA, Sterling J, Thompson C, et al. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol Cell. 2012 May 25;46(4):424-35.

Roberts SA, Lawrence MS, Klimczak LJ, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013 Sep;45(9):970-6.

Wang J, Gonzalez KD, Scaringe WA, et al. Evidence for mutation showers. Proc Natl Acad Sci U S A. 2007 May 15;104(20):8403-8.


###Example 1:
showers(position=example1, min=5, max=100)

###Example 2:
showers(position=example2, min=5, max=100)

###Example 3:

###Locate the clustered mutations;

###Locate the complex mutations;

[Package ClusteredMutations version 1.0.1 Index]