getPausingIndices {BRGenomics} | R Documentation

## Calculate pausing indices from user-supplied promoters & genebodies

### Description

Pausing index (PI) is calculated for each gene (within matched `promoters.gr` and `genebodies.gr`) as promoter-proximal (or pause region) signal counts divided by genebody signal counts. If `length.normalize = TRUE` (recommended), the signal counts within each range in `promoters.gr` and `genebodies.gr` are divided by their respective range widths (region lengths) before pausing indices are calculated.

### Usage

    getPausingIndices(
      dataset.gr,
      promoters.gr,
      genebodies.gr,
      field = "score",
      length.normalize = TRUE,
      remove.empty = FALSE,
      blacklist = NULL,
      melt = FALSE,
      region_names = NULL,
      expand_ranges = FALSE,
      ncores = getOption("mc.cores", 2L)
    )

### Arguments

`dataset.gr` | A GRanges object in which signal is contained in metadata (typically in the "score" field), or a named list of such GRanges objects.
`promoters.gr` | A GRanges object containing promoter-proximal regions of interest.
`genebodies.gr` | A GRanges object containing genebody regions of interest.
`field` | The metadata field of `dataset.gr` to be counted. If `length(field) > 1`, a dataframe is returned containing the pausing indices for each region in each field. If `field` not found in `names(mcols(dataset.gr))`, will default to using all fields found in `dataset.gr`. If `dataset.gr` is a list, a single `field` should be given, or `length(field)` should be the equal to the number of datasets in `dataset.gr`.
`length.normalize` | A logical indicating if signal counts within regions of interest should be length normalized. The default is `TRUE`, which is recommended, especially if input regions don't all have the same width.
`remove.empty` | A logical indicating if genes without any signal in `promoters.gr` should be removed. No genes are filtered by default. If `dataset.gr` is a list of datasets, or if `length(field) > 1`, regions are filtered unless they have promoter signal in all datasets.
`blacklist` | An optional GRanges object containing regions that should be excluded from signal counting. If `length.normalize = TRUE`, blacklisted positions will be excluded from length calculations. Users should take care to note if regions of interest substantially overlap blacklisted positions.
`melt` | If `melt = TRUE`, a dataframe is returned containing a column for regions and another column for pausing indices. If multiple datasets are given (if `dataset.gr` is a list or if `length(field) > 1`), the output dataframe is melted to contain a third column indicating the sample names. (See section on return values below).
`region_names` | If `melt = TRUE`, an optional vector of names for the regions in `regions.gr`. If left as `NULL`, indices of `regions.gr` are used instead.
`expand_ranges` | Logical indicating if ranges in `dataset.gr` should be treated as descriptions of single molecules (`FALSE`), or if ranges should be treated as representing multiple adjacent positions with the same signal (`TRUE`). See `getCountsByRegions`.
`ncores` | Multiple cores will only be used if `dataset.gr` is a list of multiple datasets, or if `length(field) > 1`.

### Value

A vector parallel to the input genelist, unless `remove.empty = TRUE`, in which case the vector may be shorter. If `dataset.gr` is a list, or if `length(field) > 1`, a dataframe is returned, containing a column for each field. However, if `melt = TRUE`, dataframes contain one column to indicate regions (either by their indices, or by `region_names`, if given), another column to indicate signal, and a third column containing the sample name (unless `dataset.gr` is a single GRanges object).

### Author(s)

Mike DeBerardine

### See Also

`getCountsByRegions`

### Examples

    data("PROseq") # load included PROseq data
    data("txs_dm6_chr4") # load included transcripts

    #--------------------------------------------------#
    # Get promoter-proximal and genebody regions
    #--------------------------------------------------#

    # genebodies from +300 to 300 bp before the poly-A site
    gb <- genebodies(txs_dm6_chr4, 300, -300, min.window = 400)

    # get the transcripts that are large enough (>1kb in size)
    txs <- subset(txs_dm6_chr4, tx_name %in% gb$tx_name)

    # for the same transcripts, promoter-proximal region from 0 to +100
    pr <- promoters(txs, 0, 100)

    #--------------------------------------------------#
    # Calculate pausing indices
    #--------------------------------------------------#

    pidx <- getPausingIndices(PROseq, pr, gb)

    length(txs)
    length(pidx)
    head(pidx)

    #--------------------------------------------------#
    # Without length normalization
    #--------------------------------------------------#

    head( getPausingIndices(PROseq, pr, gb, length.normalize = FALSE) )

    #--------------------------------------------------#
    # Removing empty means the values no longer match the genelist
    #--------------------------------------------------#

    pidx_signal <- getPausingIndices(PROseq, pr, gb, remove.empty = TRUE)

    length(pidx_signal)

[Package BRGenomics version 0.99.31 Index]