collapseBins {AneuFinder} | 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. If `NULL` directly adjacent bins will be collapsed.
`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

    ## Get an example BED file with single-cell-sequencing reads
    bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
    ## Bin the BAM file into bin size 1Mp
    binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
                      chromosomes=c(1:19,'X','Y'))
    ## Collapse the bins by chromosome and get average, summed and maximum read count
    df <- as.data.frame(binned[[1]])
    # Remove one bin for illustration purposes
    df <- df[-3,]
    head(df)
    collapseBins(df, column2collapseBy='seqnames', columns2sumUp=c('width','counts'),
                           columns2average='counts', columns2getMax='counts',
                           columns2drop=c('mcounts','pcounts'))
    collapseBins(df, column2collapseBy=NULL, columns2sumUp=c('width','counts'),
                           columns2average='counts', columns2getMax='counts',
                           columns2drop=c('mcounts','pcounts'))

[Package AneuFinder version 1.20.0 Index]