R/features.r

In valr: Genome Interval Arithmetic

#' Create intron features.
#'
#' Numbers in the `score` column are intron numbers from 5' to 3' independent of
#' strand. I.e., the first introns for `+` and `-` strand genes both have `score`
#' values of `1`.
#'
#' @param x [ivl_df] in BED12 format
#'
#' @family feature functions
#'
#' @examples
#' x <- read_bed12(valr_example("mm9.refGene.bed.gz"))
#'
#' create_introns(x)
#'
#' @export
create_introns <- function(x) {
  res <- bed12_to_exons(x)
  res <- group_by(res, name)
  res <- mutate(
    res,
    .start = end, .end = lead(start),
    score = ifelse(strand == "+", score, score - 1),
    start = .start, end = .end
  )
  res <- select(res, -.start, -.end)
  res <- ungroup(res)
  res <- na.omit(res)

  # remove zero length intervals
  res <- filter(res, start < end)

  res
}

#' Create 5' UTR features.
#'
#' @param x [ivl_df] in BED12 format
#'
#' @family feature functions
#'
#' @examples
#' x <- read_bed12(valr_example("mm9.refGene.bed.gz"))
#'
#' create_utrs5(x)
#'
#' @export
create_utrs5 <- function(x) {
  res <- group_by(x, name)
  res <- mutate(
    res,
    start = ifelse(strand == "+", start, cds_end),
    end = ifelse(strand == "+", cds_start, end)
  )
  res <- ungroup(res)
  res <- select(res, chrom:strand)

  # remove zero length intervals
  res <- filter(res, start < end)

  res
}

#' Create 3' UTR features.
#'
#' @param x [ivl_df] in BED12 format
#'
#' @family feature functions
#'
#' @examples
#' x <- read_bed12(valr_example("mm9.refGene.bed.gz"))
#'
#' create_utrs3(x)
#'
#' @export
create_utrs3 <- function(x) {
  res <- group_by(x, name)
  res <- mutate(
    res,
    start = ifelse(strand == "+", cds_end, start),
    end = ifelse(strand == "+", end, cds_start)
  )
  res <- ungroup(res)
  res <- select(res, chrom:strand)

  # remove zero length intervals
  res <- filter(res, start < end)

  res
}

#' Create transcription start site features.
#'
#' @param x [ivl_df] in BED format
#'
#' @family feature functions
#'
#' @examples
#' x <- read_bed12(valr_example("mm9.refGene.bed.gz"))
#'
#' create_tss(x)
#'
#' @export
create_tss <- function(x) {
  res <- group_by(x, name)
  res <- mutate(
    res,
    start = ifelse(strand == "+", start, end - 1),
    end = ifelse(strand == "+", start + 1, end)
  )
  res <- ungroup(res)
  res <- select(res, chrom:strand)
  res
}