Aneufinder {AneuFinder} | R Documentation

## Wrapper function for the `AneuFinder` package

### Description

This function is an easy-to-use wrapper to bin the data, find copy-number-variations, locate breakpoints, plot genomewide heatmaps, distributions, profiles and karyograms.

### Usage

    Aneufinder(inputfolder, outputfolder, configfile = NULL, numCPU = 1,
      reuse.existing.files = TRUE, binsizes = 1e+06, stepsizes = binsizes,
      variable.width.reference = NULL, reads.per.bin = NULL,
      pairedEndReads = FALSE, assembly = NULL, chromosomes = NULL,
      remove.duplicate.reads = TRUE, min.mapq = 10, blacklist = NULL,
      use.bamsignals = FALSE, reads.store = FALSE, correction.method = NULL,
      GC.BSgenome = NULL, method = c("edivisive"), strandseq = FALSE,
      R = 10, sig.lvl = 0.1, eps = 0.01, max.time = 60, max.iter = 5000,
      num.trials = 15, states = c("zero-inflation", paste0(0:10, "-somy")),
      confint = NULL, refine.breakpoints = FALSE, hotspot.bandwidth = NULL,
      hotspot.pval = 0.05, cluster.plots = TRUE)

### Arguments

`inputfolder` | Folder with either BAM or BED files.
`outputfolder` | Folder to output the results. If it does not exist it will be created.
`configfile` | A file specifying the parameters of this function (without `inputfolder`, `outputfolder` and `configfile`). Having the parameters in a file can be handy if many samples with the same parameter settings are to be run. If a `configfile` is specified, it will take priority over the command line parameters.
`numCPU` | The numbers of CPUs that are used. Should not be more than available on your machine.
`reuse.existing.files` | A logical indicating whether or not existing files in `outputfolder` should be reused.
`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"`.
`variable.width.reference` | A BAM file that is used as reference to produce variable width bins. See `variableWidthBins` for details.
`reads.per.bin` | Approximate number of desired reads per bin. The bin size will be selected accordingly. Output files are produced for each value.
`pairedEndReads` | Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).
`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'.
`chromosomes` | If only a subset of the chromosomes should be imported, specify them here.
`remove.duplicate.reads` | A logical indicating whether or not duplicate reads should be removed.
`min.mapq` | Minimum mapping quality when importing from BAM files. Set `min.mapq=NA` to keep all reads.
`blacklist` | A `GRanges-class` or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.
`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.
`reads.store` | Set `reads.store=TRUE` to store read fragments as RData in folder 'data' and as BED files in 'BROWSERFILES/data'. This option will force `use.bamsignals=FALSE`.
`correction.method` | Correction methods to be used for the binned read counts. Currently only `'GC'`.
`GC.BSgenome` | A `BSgenome` object which contains the DNA sequence that is used for the GC correction.
`method` | Any combination of `c('HMM','dnacopy','edivisive')`. Option `method='HMM'` uses a Hidden Markov Model as described in doi:10.1186/s13059-016-0971-7 to call copy numbers. Option `'dnacopy'` uses `segment` from the DNAcopy package to call copy numbers similarly to the method proposed in doi:10.1038/nmeth.3578, which gives more robust but less sensitive results compared to the HMM. Option `'edivisive'` (DEFAULT) works like option `'dnacopy'` but uses the `e.divisive` function from the ecp package for segmentation.
`strandseq` | A logical indicating whether the data comes from Strand-seq experiments. If `TRUE`, both strands carry information and are treated separately.
`R` | method-edivisive: The maximum number of random permutations to use in each iteration of the permutation test (see `e.divisive`). Increase this value to increase accuracy on the cost of speed.
`sig.lvl` | method-edivisive: The level at which to sequentially test if a proposed change point is statistically significant (see `e.divisive`). Increase this value to find more breakpoints.
`eps` | method-HMM: Convergence threshold for the Baum-Welch algorithm.
`max.time` | method-HMM: The maximum running time in seconds for the Baum-Welch algorithm. If this time is reached, the Baum-Welch will terminate after the current iteration finishes. Set `max.time = -1` for no limit.
`max.iter` | method-HMM: The maximum number of iterations for the Baum-Welch algorithm. Set `max.iter = -1` for no limit.
`num.trials` | method-HMM: The number of trials to find a fit where state `most.frequent.state` is most frequent. Each time, the HMM is seeded with different random initial values.
`states` | method-HMM: A subset or all of `c("zero-inflation","0-somy","1-somy","2-somy","3-somy","4-somy",...)`. This vector defines the states that are used in the Hidden Markov Model. The order of the entries must not be changed.
`confint` | Desired confidence interval for breakpoints. Set `confint=NULL` to disable confidence interval estimation. Confidence interval estimation will force `reads.store=TRUE`.
`refine.breakpoints` | A logical indicating whether breakpoints from the HMM should be refined with read-level information. `refine.breakpoints=TRUE` will force `reads.store=TRUE`.
`hotspot.bandwidth` | A vector the same length as `binsizes` with bandwidths for breakpoint hotspot detection (see `hotspotter` for further details). If `NULL`, the bandwidth will be chosen automatically as the average distance between reads.
`hotspot.pval` | P-value for breakpoint hotspot detection (see `hotspotter` for further details). Set `hotspot.pval = NULL` to skip hotspot detection.
`cluster.plots` | A logical indicating whether plots should be clustered by similarity.

### Value

`NULL`

### Author(s)

Aaron Taudt

### Examples

    ## Not run:
    ## The following call produces plots and genome browser files for all BAM files in "my-data-folder"
    Aneufinder(inputfolder="my-data-folder", outputfolder="my-output-folder")
    ## End(Not run)

[Package AneuFinder version 1.12.1 Index]