Compute k-mer distribution in genomic intervals

Source: R/sequence.R

Counts the occurrence of all k-mers (of size k) within the specified genomic intervals, optionally excluding masked regions.

gseq.kmer.dist(intervals, k = 6L, mask = NULL)

Arguments

intervals

Genomic intervals to analyze

k

Integer k-mer size (1-10). Default is 6.

mask

Optional intervals to exclude from counting. Positions within the mask will not contribute to k-mer counts.

Value

A data frame with columns:

kmer

Character string representing the k-mer sequence

count

Number of occurrences of this k-mer

Only k-mers with count > 0 are included. K-mers containing N bases are not counted.

Examples

gdb.init_examples()

# Count all 6-mers in first 10kb of chr1
intervals <- data.frame(chrom = "chr1", start = 0, end = 10000)
kmer_dist <- gseq.kmer.dist(intervals, k = 6)
head(kmer_dist)
#>     kmer count
#> 1 AAAAAA     3
#> 2 AAAAAG     2
#> 3 AAAAAT     4
#> 4 AAAACA     1
#> 5 AAAACC     2
#> 6 AAAAGA     1

# Count dinucleotides
dinucs <- gseq.kmer.dist(intervals, k = 2)
dinucs
#>    kmer count
#> 1    AA   479
#> 2    AC   519
#> 3    AG   801
#> 4    AT   292
#> 5    CA   760
#> 6    CC  1087
#> 7    CG   277
#> 8    CT   881
#> 9    GA   574
#> 10   GC   835
#> 11   GG   982
#> 12   GT   475
#> 13   TA   278
#> 14   TC   565
#> 15   TG   806
#> 16   TT   388

# Count with mask
mask <- data.frame(chrom = "chr1", start = 5000, end = 6000)
kmer_dist_masked <- gseq.kmer.dist(intervals, k = 6, mask = mask)