R/Rcpp_interface.R

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

# This file was generated by Rcpp::compileAttributes
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

# == title
# Find intervals by binary search
#
# == param
# -breaks a non-decreasing integer vector
# -search an integer vector
# -left_index whether to use the index of left break or right break
#
# == value
# A vector of index.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# site = c(2, 5, 9, 10, 15, 20)
# binary_search(site, c(1, 5, 12, 30), FALSE)
# binary_search(site, c(1, 5, 12, 30), TRUE)
binary_search = function(breaks, search, left_index = TRUE) {
    .Call('epic_binary_search', PACKAGE = 'epic', breaks, search, left_index) + 1
}

# == title
# Extract subset of sites in a set of intervals
#
# == param
# -start      start positions, a numeric vector
# -end        end positions, a numeric vector.
# -site       positions of all sites, should be sorted increasingly.
# -return_index   whether return the index in the position vector or just the position itself?
# -min_sites  minimal number of sites in an interval, regions which contain sites less than this value will be filtered out.
#
# == details
# Providing a huge vector of genomic positions, we want to extract subset of positions which
# locate in a specific group of regions (e.g. extract CpG sites in DMRs). Normally, we will use:
#
# 	site = sort(sample(10000000, 1000000))
# 	start = 123456
# 	end = 654321
# 	subsite = site[site >= start & site <= end]
#
# Unfortunately, in above code, the whole vector ``site`` will be scanned four times
# (``>=``, ``<=``, ``&`` and ``[``).
# If you want to look for sites in more than one regions (e.g. 1000 regions), in every
# loop, the whole ``site`` vector will be re-scanned again and again which is very time-consuming.
#
# Here we have `extract_sites` function which uses binary search to do subsetting.
# Of course, ``site`` should be sorted non-decreasing beforehand.
#
#   subsite = extract_sites(start, end, site, index = FALSE)
#
# Not only for single interval, you can also extract sites in multiple genomic regins,
# by setting ``start`` and ``end`` as vectors.
#
#   start = c(123456, 234567, 345678)
#   end = c(133456, 244567, 355678)
#   subsite = extract_sites(start, end, site)
#
# You can choose to return index only or positions.
#
#   subsite = extract_sites(start, end, site, return_index = FALSE)
#   head(subsite)
#   subsite_index = extract_sites(start, end, site, return_index = TRUE)
#   head(subsite_index)
#   head(site[subsite_index])
#
# Regions that include sites less than ``min_site`` will be filtered out.
#
# == value
# A vector of positions or index.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# site = sort(sample(1000, 100))
# pos = do.call("rbind", lapply(1:10, function(i) sort(sample(max(site), 2))))
# extract_sites(pos[, 1], pos[, 2], site)
extract_sites = function(start, end, site, return_index = FALSE, min_sites = 0) {
    .Call('epic_extract_sites', PACKAGE = 'epic', start, end, site, return_index, min_sites)
}

rowWhichMax = function(m) {
    .Call('epic_rowWhichMax', PACKAGE = 'epic', m)
}