example_kmeRtone_score: Example 2-mer enrichment/depletion scores

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Example 2-mer enrichment/depletion scores

Description

Below is an example code that generates random genomic coordinates and runs the default kmeRtone SCORE function to quantify the k-meric enrichment and depletion.

Usage

example_kmeRtone_score

Format

A data frame with 1001 rows and 3 columns

case

Case k-mers, e.g. damage k-mer counts

case_skew

Case k-mers skews, e.g. skew of the damage k-mers counts

control

control k-mers, e.g. damage k-mer counts

control_skew

control k-mers skews, e.g. skew of the damage k-mers counts

kmer

K-meric sequence

z

Intrinsic susceptibility z-score for each k-mer

Source

https://github.com/SahakyanLab/kmeRtone/blob/master/README.md

Examples

# 1. Randomly generate genomic positions and save results
library(data.table)
library(kmeRtone)
temp_dir <- tempdir()

set.seed(1234)
temp_files <- character(1)
for(chr in 1){
    genomic_coor <- data.table(
        seqnames = paste0("chr", chr),
        start = sample(
            x = 10000:10000000, 
            size = 100000, 
            replace = FALSE
        ),
        width = 2
    )

    f <- file.path(temp_dir, paste0("chr", chr, ".csv"))
    fwrite(genomic_coor, f)
    temp_files[chr] <- f
}

# 2. Run kmeRtone score function
temp_dir_genome <- tempdir()
kmeRtone::kmeRtone(
    case.coor.path = temp_dir, 
    genome.name = "hg19", 
    genome.path = temp_dir_genome,
    strand.sensitive = FALSE, 
    k = 2,
    ctrl.rel.pos = c(80, 500),
    case.pattern = NULL,
    single.case.len = 2,
    output.dir = temp_dir,
    module = "score",
    rm.case.kmer.overlaps = FALSE,
    merge.replicate = TRUE, 
    kmer.table = NULL,
    verbose = TRUE
)

# 3. Clean up temporary files
rm_files <- file.remove(temp_files)

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.