mutclusters: mutclusters

In mskilab/skitools: Various mskilab R utilties

mutclusters

Description

Returns genes with a degree of mutaiton clustering (e.g. ranked by how many k>k.thresh clusters with d<d.thresh pairwise distance, or the largest cluster with those characteristics)

if max.cluster = TRUE returns maximum size cluster in gene where either all (method == complete) or at least one (method single) mutation pair is within distance d

if max.cluster = F then returns number of clusters of mutations of count greater than k within a distance d per gene

eg d = 0, k = 1, will give the number of unique sites with more than 1 perfectly recurrent mutation per gene

Clustering is by default using single-linkage agglomerative clustering, but any method that is input to hclust can be used

Usage

mutclusters(maf, d = 0, k = 1, method = "single", max.cluster = TRUE)

Arguments

maf	maf data.frame
d	max distance threshold in amino acid space
k	minimum number of mutations in returned clusters
method	character specifying "single" or "complete" linkage clustering of mutations
max.cluster	logical flag whether to return the gene with the largest cluster (if TRUE) or the most number of clusters (if FALSE) (=TRUE)

Value

genes ranked by numbers of cluster or max.cluster size

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.