clusterCounts: Count occurrences of k-mer clusters

In sarks: Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Description

Counts how often any k-mer from a cluster of k-mers (or list of clusters of k-mers) occurs in each element of a character vector.

Usage

clusterCounts(kmers, seqs, directional = TRUE, overlap = FALSE)

Arguments

kmers	character vector or XStringSet of k-mers composing cluster to search for, or a named list of such character vectors or XStringSet objects to count multiple clusters.
seqs	character vector or XStringSet of sequences in which to search for and count occurrences of kmers.
directional	logical value: if FALSE, counts occurrences of either cluster(s) of k-mers or their reverse-complements. Makes sense only if applying to DNA sequences!
overlap	logical value: should overlapping occurrences of k-mers be counted as multiple hits?

Value

if cluster is a single character vector or XStringSet (of any length), returns integer vector of counts; if cluster is a list of character vectors, returns matrix of counts: one row per sequence in seqs, one column per character vector/XStringSet in cluster

Examples

seqs <- c(
    line1 = "My mind's got a mind of its own",
    line2 = "Takes me out to parties when I'd rather be alone",
    line3 = "Takes me out a-walkin' when I'd rather be at home"
)
clusters <- list(
    antisocial = c('alone', 'at home'),
    mind = 'mind'
)
clCounts <- clusterCounts(clusters, seqs)

sarks documentation built on Nov. 8, 2020, 6:54 p.m.