generate_similarity_table: Generates a table of similarity measures between two sets of...

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Generates a table of similarity measures between two sets of peaks

Description

Goes through the set of genes contained in peaks.1. For each gene-specific peak, calculate the amount of overlapping nucleotides to the nearest peak in peaks.2. If the gene is not available in peaks.2, ditance is set to -1e7.

Usage

generate_similarity_table(peaks.1, peaks.2, ncores = 1)

Arguments

peaks.1	first set of peaks - used as a reference point
peaks.2	second set of peaks being compared
ncores	number of cores for multithreading (default 1)

Value

a data-frame with peaks from peaks.1 mapped to the closest corresponding peak in peaks.2.

Examples

## Not run: 
extdata_path <- system.file("extdata",package = "Sierra")
peak.sites.file <- paste0(extdata_path,"/TIP_merged_peaks.txt")
peak.table <- read.table(peak.sites.file, sep="\t", header = TRUE, stringsAsFactors = FALSE)

generate_similarity_table(peak.table, peak.table)

## End(Not run)

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.