binReads {AneuFinder} | R Documentation

## Convert aligned reads from various file formats into read counts in equidistant bins

### Description

Convert aligned reads in .bam or .bed(.gz) format into read counts in equidistant windows.

### Usage

    binReads(file, assembly, ID = basename(file), bamindex = file,
      chromosomes = NULL, pairedEndReads = FALSE, min.mapq = 10,
      remove.duplicate.reads = TRUE, max.fragment.width = 1000,
      blacklist = NULL, outputfolder.binned = "binned_data", binsizes = 1e+06,
      stepsizes = NULL, reads.per.bin = NULL, reads.per.step = NULL,
      bins = NULL, variable.width.reference = NULL, save.as.RData = FALSE,
      calc.complexity = TRUE, call = match.call(), reads.store = FALSE,
      outputfolder.reads = "data", reads.return = FALSE,
      reads.overwrite = FALSE, reads.only = FALSE, use.bamsignals = FALSE)

### Arguments

`file` | A file with aligned reads. Alternatively a `GRanges-class` with aligned reads.
`assembly` | Please see `fetchExtendedChromInfoFromUCSC` for available assemblies. Only necessary when importing BED files. BAM files are handled automatically. Alternatively a data.frame with columns 'chromosome' and 'length'.
`ID` | An identifier that will be used to identify the file throughout the workflow and in plotting.
`bamindex` | BAM index file. Can be specified without the .bai ending. If the index file does not exist it will be created and a warning is issued.
`chromosomes` | If only a subset of the chromosomes should be binned, specify them here.
`pairedEndReads` | Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).
`min.mapq` | Minimum mapping quality when importing from BAM files. Set `min.mapq=NA` to keep all reads.
`remove.duplicate.reads` | A logical indicating whether or not duplicate reads should be removed.
`max.fragment.width` | Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.
`blacklist` | A `GRanges-class` or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.
`outputfolder.binned` | Folder to which the binned data will be saved. If the specified folder does not exist, it will be created.
`binsizes` | An integer vector with bin sizes. If more than one value is given, output files will be produced for each bin size.
`stepsizes` | A vector of step sizes the same length as `binsizes`. Only used for `method="HMM"`.
`reads.per.bin` | Approximate number of desired reads per bin. The bin size will be selected accordingly. Output files are produced for each value.
`reads.per.step` | Approximate number of desired reads per step.
`bins` | A named `list` with `GRanges-class` containing precalculated bins produced by `fixedWidthBins` or `variableWidthBins`. Names must correspond to the binsize.
`variable.width.reference` | A BAM file that is used as reference to produce variable width bins. See `variableWidthBins` for details.
`save.as.RData` | If set to `FALSE`, no output file will be written. Instead, a GenomicRanges object containing the binned data will be returned. Only the first binsize will be processed in this case.
`calc.complexity` | A logical indicating whether or not to estimate library complexity.
`call` | The `match.call()` of the parent function.
`reads.store` | If `TRUE` processed read fragments will be saved to file. Reads are processed according to `min.mapq` and `remove.duplicate.reads`. Paired end reads are coerced to single end fragments. Will be ignored if `use.bamsignals=TRUE`.
`outputfolder.reads` | Folder to which the read fragments will be saved. If the specified folder does not exist, it will be created.
`reads.return` | If `TRUE` no binning is done and instead, read fragments from the input file are returned in `GRanges-class` format.
`reads.overwrite` | Whether or not an existing file with read fragments should be overwritten.
`reads.only` | If `TRUE` only read fragments are stored and/or returned and no binning is done.
`use.bamsignals` | If `TRUE` the bamsignals package will be used for binning. This gives a tremendous performance increase for the binning step. `reads.store` and `calc.complexity` will be set to `FALSE` in this case.

### Details

Convert aligned reads from .bam or .bed(.gz) files into read counts in equidistant windows (bins). This function uses `GenomicRanges::countOverlaps` to calculate the read counts.

### Value

The function produces a `list()` of `GRanges-class` or `GRangesList` objects with meta data columns 'counts', 'mcounts', 'pcounts' that contain the total, minus and plus read count. This binned data will be either written to file (`save.as.RData=FALSE`) or given as return value (`save.as.RData=FALSE`).

### See Also

binning

### 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 BED file into bin size 1Mb
    binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
                      chromosomes=c(1:19,'X','Y'))
    print(binned)

[Package AneuFinder version 1.12.1 Index]