collapseBins {chromstaR} | R Documentation

## Collapse consecutive bins

### Description

The function will collapse consecutive bins which have, for example, the same combinatorial state.

### Usage

    collapseBins(
      data,
      column2collapseBy = NULL,
      columns2sumUp = NULL,
      columns2average = NULL,
      columns2getMax = NULL,
      columns2drop = NULL
    )

### Arguments

`data` | A data.frame containing the genomic coordinates in the first three columns.
`column2collapseBy` | The number of the column which will be used to collapse all other inputs. If a set of consecutive bins has the same value in this column, they will be aggregated into one bin with adjusted genomic coordinates.
`columns2sumUp` | Column numbers that will be summed during the aggregation process.
`columns2average` | Column numbers that will be averaged during the aggregation process.
`columns2getMax` | Column numbers where the maximum will be chosen during the aggregation process.
`columns2drop` | Column numbers that will be dropped after the aggregation process.

### Details

The following tables illustrate the principle of the collapsing:

Input data:

seqnames | start | end | column2collapseBy | moreColumns | columns2sumUp
chr1 | 0 | 199 | 2 | 1 10 | 1 3
chr1 | 200 | 399 | 2 | 2 11 | 0 3
chr1 | 400 | 599 | 2 | 3 12 | 1 3
chr1 | 600 | 799 | 1 | 4 13 | 0 3
chr1 | 800 | 999 | 1 | 5 14 | 1 3

Output data:

seqnames | start | end | column2collapseBy | moreColumns | columns2sumUp
chr1 | 0 | 599 | 2 | 1 10 | 2 9
chr1 | 600 | 999 | 1 | 4 13 | 1 6

### Value

A data.frame.

### Author(s)

Aaron Taudt

### Examples

    ## Load example data
    ## Get an example multiHMM
    file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                        package="chromstaR")
    model <- get(load(file))
    df <- as.data.frame(model$bins)
    shortdf <- collapseBins(df, column2collapseBy='state', columns2sumUp='width', columns2average=6:9)

[Package chromstaR version 1.20.2 Index]