removeData {recoup} | R Documentation

## Remove data from recoup list object

### Description

This function clears members of the `recoup` output object that must be cleared in order to apply a new set of parameters without completely rerunning `recoup`.

### Usage

        removeData(input, type = c("ranges", "coverage",
            "profile", "reference"))

### Arguments

`input` | a list object created from `recoup` or its `data` member.
`type` | one of `"ranges"`, `"coverage"`, `"profile"`, `"reference"`.

### Details

This function clears members of the `recoup` output object which typically take some time to be calculated but it is necessary to clean them if the user wants to change input parameters that cause recalculations of these members. For example, if the user changes the `binParams`, the profile matrices (`"profile"` object member) have to be recalculated.

`type` controls what data will be removed. `"ranges"` removes the reads imported from BAM/BED files. This is useful when for example the normalization method is changed. `"coverage"` removes the calculated coverages over the reference genomic regions. This is required again when the normalization method changes. `"profile"` removes the profile matrices derived from coverages. This is required for example when the `binParams` main argument changes. Finally, `"reference"` removes the genomic loci over which the calculations are taking place. This is required when the `genome`, `refdb` or `version` main arguments change.

### Value

A list which is normally the output of `recoup` without the members that have been removed from it.

### Author(s)

Panagiotis Moulos

### Examples

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

    # Before removing
    names(test.input)

    # Remove a member
    test.input <- removeData(test.input,"ranges")

    # Removed
    names(test.input)

[Package recoup version 1.20.1 Index]