reduceByFile {GenomicFiles} | R Documentation

## Parallel computations by files

### Description

Computations are distributed in parallel by file. Data subsets are extracted and manipulated (MAP) and optionally combined (REDUCE) within a single file.

### Usage

    ## S4 method for signature 'GRanges,ANY'
    reduceByFile(ranges, files, MAP,
        REDUCE, ..., summarize=FALSE, iterate=TRUE, init)
    ## S4 method for signature 'GRangesList,ANY'
    reduceByFile(ranges, files, MAP,
        REDUCE, ..., summarize=FALSE, iterate=TRUE, init)
    ## S4 method for signature 'GenomicFiles,missing'
    reduceByFile(ranges, files, MAP,
        REDUCE, ..., summarize=FALSE, iterate=TRUE, init)

    reduceFiles(ranges, files, MAP, REDUCE, ..., init)

### Arguments

`ranges` | A `GRanges`, `GrangesList` or `GenomicFiles` object. A `GRangesList` implies a grouping of the ranges; `MAP` is applied to each element of the `GRangesList` vs each range when `ranges` is a `GRanges`. When `ranges` is a `GenomicFiles` the `files` argument is missing; both ranges and files are extracted from the object.
`files` | A `character` vector or `List` of filenames. A `List` implies a grouping of the files; `MAP` is applied to each element of the `List` vs each file individually.
`MAP` | A function executed on each worker. The signature must contain a minimum of two arguments representing the ranges and files. There is no restriction on argument names and additional arguments can be provided. `MAP = function(range, file, ...)`
`REDUCE` | An optional function that combines output from the `MAP` step. The signature must contain at least one argument representing the list output from `MAP`. There is no restriction on argument names and additional arguments can be provided. `REDUCE = function(mapped, ...)` Reduction combines data from a single worker and is always performed as part of the distributed step. When `iterate=TRUE` `REDUCE` is applied after each `MAP` step; depending on the nature of `REDUCE`, iterative reduction can substantially decrease the data stored in memory. When `iterate=FALSE` reduction is applied to the list of `MAP` output applied to all files / ranges. When `REDUCE` is missing, output is a list from `MAP`.
`iterate` | A logical indicating if the `REDUCE` function should be applied iteratively to the output of `MAP`. When `REDUCE` is missing `iterate` is set to FALSE. This argument applies to `reduceByFile` only (`reduceFiles` calls MAP a single time on each worker). Collapsing results iteratively is useful when the number of records to be processed is large (maybe complete files) but the end result is a much reduced representation of all records. Iteratively applying `REDUCE` reduces the amount of data on each worker at any one time and can substantially reduce the memory footprint.
`summarize` | A logical indicating if results should be returned as a `SummarizedExperiment` object instead of a list; data are returned in the `assays` slot named 'data'. This argument applies to `reduceByFile` only. When `REDUCE` is provided `summarize` is ignored (i.e., set to FALSE). A `SummarizedExperiment` requires the number of rows in `rowRanges` and `assays` to match. Because `REDUCE` collapses the data across ranges, the dimension of the result no longer matches that of the original ranges.
`init` | An optional initial value for `REDUCE` when `iterate=TRUE`. `init` must be an object of the same type as the elements returned from `MAP`. `REDUCE` logically adds `init` to the start (when proceeding left to right) or end of results obtained with `MAP`.
`...` | Arguments passed to other methods.

### Details

`reduceByFile` extracts, manipulates and combines multiple ranges within a single file. Each file is sent to a worker where `MAP` is invoked on each file / range combination. This approach allows multiple ranges extracted from a single file to be kept separate or combined with `REDUCE`.

In contrast, `reduceFiles` treats the output of all MAP calls as a group and reduces them together. `REDUCE` usually plays a minor role by concatenating or unlisting results.

Both `MAP` and `REDUCE` are applied in the distributed step (“on the worker“). Results are not combined across workers in the distributed step.

### Value

- reduceByFile: When `summarize=FALSE` the return value is a `list` or the value from the final invocation of `REDUCE`. When `summarize=TRUE` output is a `SummarizedExperiment`. When `ranges` is a `GenomicFiles` object data from `rowRanges`, `colData` and `metadata` are transferred to the `SummarizedExperiment`.

- reduceFiles: A `list` or the value returned by the final invocation of `REDUCE`.

### Author(s)

Martin Morgan and Valerie Obenchain

### See Also

- reduceRanges

- reduceByRange

- GenomicFiles-class

### Examples

    if (requireNamespace("RNAseqData.HNRNPC.bam.chr14", quietly=TRUE)) {
      ## -----------------------------------------------------------------------
      ## Count junction reads in BAM files
      ## -----------------------------------------------------------------------
      fls <-                                      ## 8 bam files
          RNAseqData.HNRNPC.bam.chr14::RNAseqData.HNRNPC.bam.chr14_BAMFILES

      ## Ranges of interest.
      gr <- GRanges("chr14", IRanges(c(19100000, 106000000), width=1e7))

      ## MAP outputs a table of junction counts per range.
      MAP <- function(range, file, ...) {
          ## for readGAlignments(), Rsamtools::ScanBamParam()
          requireNamespace("GenomicAlignments", quietly=TRUE)
          param = Rsamtools::ScanBamParam(which=range)
          gal = GenomicAlignments::readGAlignments(file, param=param)
          table(GenomicAlignments::njunc(gal))
      }

      ## -----------------------------------------------------------------------
      ## reduceByFile:

      ## With no REDUCE, counts are computed for each range / file combination.
      counts1 <- reduceByFile(gr, fls, MAP)
      length(counts1)          ## 8 files
      elementNROWS(counts1)    ## 2 ranges each

      ## Tables of counts for each range:
      counts1[[1]]

      ## With a REDUCE, results are combined on the fly. This reducer sums the
      ## number of records in each range with exactly 1 junction.
      REDUCE <- function(mapped, ...)
          sum(sapply(mapped, "[", "1"))

      reduceByFile(gr, fls, MAP, REDUCE)

      ## -----------------------------------------------------------------------
      ## reduceFiles:

      ## All ranges are treated as a single group:
      counts2 <- reduceFiles(gr, fls, MAP)

      ## Counts are for all ranges grouped:
      counts2[[1]]

      ## Contrast the above with that from reduceByFile() where counts
      ## are for each range separately:
      counts1[[1]]

      ## -----------------------------------------------------------------------
      ## Methods for the GenomicFiles class:

      ## Both reduceByFiles() and reduceFiles() can operate on a GenomicFiles
      ## object.
      colData <- DataFrame(method=rep("RNASeq", length(fls)),
                           format=rep("bam", length(fls)))
      gf <- GenomicFiles(files=fls, rowRanges=gr, colData=colData)
      gf

      ## Subset on ranges or files for different experimental runs.
      dim(gf)
      gf_sub <- gf[2, 3:4]
      dim(gf_sub)

      ## When summarize = TRUE and no REDUCE is given, the output is a
      ## SummarizedExperiment object.
      se <- reduceByFile(gf, MAP=MAP, summarize=TRUE)
      se

      ## Data from the rowRanges, colData and metadata slots in the
      ## GenomicFiles are transferred to the SummarizedExperiment.
      colData(se)

      ## Results are in the assays slot named 'data'.
      assays(se)
    }

[Package GenomicFiles version 1.28.0 Index]