getCountsByPositions {BRGenomics} | R Documentation

## Get signal counts at each position within regions of interest

### Description

Get the sum of the signal in `dataset.gr` that overlaps each position within each range in `regions.gr`. If binning is used (i.e. positions are wider than 1 bp), any function can be used to summarize the signal overlapping each bin. For a description of the critical difference between `expand_ranges = FALSE` and `expand_ranges = TRUE`, see `getCountsByRegions`.

### Usage

    getCountsByPositions(
      dataset.gr,
      regions.gr,
      binsize = 1,
      FUN = sum,
      simplify.multi.widths = c("error", "list", "pad 0", "pad NA"),
      field = "score",
      NF = NULL,
      blacklist = NULL,
      NA_blacklisted = FALSE,
      melt = FALSE,
      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.
`regions.gr` | A GRanges object containing regions of interest.
`binsize` | Size of bins (in bp) to use for counting within each range of `regions.gr`. Note that counts will not be length-normalized.
`FUN` | If `binsize > 1`, the function used to aggregate the signal within each bin. By default, the signal is summed, but any function operating on a numeric vector can be used.
`simplify.multi.widths` | A string indicating the output format if the ranges in `regions.gr` have variable widths. By default, an error is returned. See details below.
`field` | The metadata field of `dataset.gr` to be counted. If `length(field) > 1`, the output is a list whose elements contain the output for generated each field. If `field` not found in `names(mcols(dataset.gr))`, will default to using all fields found in `dataset.gr`.
`NF` | An optional normalization factor by which to multiply the counts. If given, `length(NF)` must be equal to `length(field)`.
`blacklist` | An optional GRanges object containing regions that should be excluded from signal counting.
`NA_blacklisted` | A logical indicating if NA values should be returned for blacklisted regions. By default, signal in the blacklisted sites is ignored, i.e. the reads are excluded. If `NA_blacklisted = TRUE`, those positions are set to `NA` in the final output.
`melt` | A logical indicating if the count matrices should be melted. If set to `TRUE`, a dataframe is returned in containing columns for "region", "position", and "signal". If `dataset.gr` is a list of multiple GRanges, or if `length(field) > 1`, a single dataframe is returned, which contains an additional column "sample", which contains individual sample names. If used with multi-width `regions.gr`, the resulting dataframe will only contain positions that are found within each respective region.
`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

If the widths of all ranges in `regions.gr` are equal, a matrix is returned that contains a row for each region of interest, and a column for each position (each base if `binsize = 1`) within each region. If `dataset.gr` is a list, a parallel list is returned containing a matrix for each input dataset.

### Use of multi-width regions of interest

If the input `regions.gr` contains ranges of varying widths, setting `simplify.multi.widths = "list"` will output a list of variable-length vectors, with each vector corresponding to an individual input region. If `simplify.multi.widths = "pad 0"` or `"pad NA"`, the output is a matrix containing a row for each range in `regions.gr`, but the number of columns is determined by the largest range in `regions.gr`. For each region of interest, columns that correspond to positions outside of the input range are set, depending on the argument, to `0` or `NA`.

### Author(s)

Mike DeBerardine

### See Also

`getCountsByRegions`, `metaSubsample`

### Examples

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

    #--------------------------------------------------#
    # counts from 0 to 50 bp after the TSS
    #--------------------------------------------------#

    txs_pr <- promoters(txs_dm6_chr4, 0, 50) # first 50 bases
    countsmat <- getCountsByPositions(PROseq, txs_pr)
    countsmat[10:15, 41:50] # show only 41-50 bp after TSS

    #--------------------------------------------------#
    # redo with 10 bp bins from 0 to 100
    #--------------------------------------------------#

    # column 5 is sums of rows shown above

    txs_pr <- promoters(txs_dm6_chr4, 0, 100)
    countsmat <- getCountsByPositions(PROseq, txs_pr, binsize = 10)
    countsmat[10:15, ]

    #--------------------------------------------------#
    # same as the above, but with the average signal in each bin
    #--------------------------------------------------#

    countsmat <- getCountsByPositions(PROseq, txs_pr, binsize = 10, FUN = mean)
    countsmat[10:15, ]

    #--------------------------------------------------#
    # standard deviation of signal in each bin
    #--------------------------------------------------#

    countsmat <- getCountsByPositions(PROseq, txs_pr, binsize = 10, FUN = sd)
    round(countsmat[10:15, ], 1)

[Package BRGenomics version 1.4.0 Index]