sliceObj {recoup} | R Documentation

## Subset recoup output list objects

### Description

This function takes as input argument an output object from `recoup` and subsets it according to the inputs `i,j,k`. The attached plots may or may not be recalculated. Other input parameters stores in `obj$callopts` are not changed apart from any `selector` option which is dropped. Note that when slicing vertically (by `j`), the `$coverage` member of the input data (if present) is not sliced, but remains as is. You can drop it using `removeData` as it is used to recalculate profile matrices only if bin sizes are changed in a `recoup` call.

### Usage

        sliceObj(obj, i = NULL, j = NULL, k = NULL,
            dropPlots = FALSE, rc = NULL)

### Arguments

`obj` | a list object created from `recoup`.
`i` | vector of numeric or character indices, corresponding to the index or rownames or names of reference genomic regions. The `design` object member will also be subset. If there is a `selector` attached to the input object (see `recoup` arguments) it will be dropped.
`j` | vector of numeric indices corresponding to the profile matrix vertical index (or base pair position or bin of base pairs) so as to subset the profile. The function will do its best to "guess" new plotting x-axis labels.
`k` | vector of numeric or character indices corresponding to sample index or sample names. These will be returned.
`dropPlots` | if profile and/or heatmap plots are attached to the input object, they will be recalculated if `dropPlots=="TRUE"` (default) or dropped otherwise

.

`rc` | fraction (0-1) of cores to use in a multicore system. It defaults to `NULL` (no parallelization).

### Value

A `recoup` list object, susbet according to `i, j`.

### Author(s)

Panagiotis Moulos

### Examples

    # Load some data
    data("recoup_test_data",package="recoup")

    # Calculate coverages
    test.tss <- recoup(
        test.input,
        design=NULL,
        region="tss",
        type="chipseq",
        genome=test.genome,
        flank=c(2000,2000),
        selector=NULL,
        plotParams=list(plot=FALSE,profile=TRUE,
            heatmap=TRUE,device="x11"),
        rc=0.5
    )

    # Plot coverage profiles
    o <- sliceObj(test.tss,i=1:10,k=1)

[Package recoup version 1.12.0 Index]