R/library.R

In GenomicInteractions: Utilities for handling genomic interaction data

# Capitalize first letter of string This function will capitalize the first letter of each string in a character vector, and lowercase
# following letters.  @param x A character vector @return a string with the first letter capitalised
capitalize <- function(x) {
    paste0(toupper(substr(x, 1, 1)), tolower(substring(x, 2)))
}

#' @importFrom GenomeInfoDb seqinfo seqlevels 'seqlevels<-' seqlengths genome isCircular 

.isEqualSeqInfo <- function(one, two) {
    seqinfo.one <- seqinfo(one)
    seqinfo.two <- seqinfo(two)
    if (length(seqinfo.one) != length(seqinfo.two)) {
        value <- FALSE
    } else {
        chr <- all(seqlevels(seqinfo.one) == seqlevels(seqinfo.two), na.rm = TRUE)
        len <- all(seqlengths(seqinfo.one) == seqlengths(seqinfo.two), na.rm = TRUE)
        cir <- all(isCircular(seqinfo.one) == isCircular(seqinfo.two), na.rm = TRUE)
        gen <- all(genome(seqinfo.one) == genome(seqinfo.two), na.rm = TRUE)
        value <- chr & len & cir & gen
    }
    return(value)
}