dba {DiffBind} | R Documentation

## Construct a DBA object

### Description

Constructs a new DBA object from a sample sheet, or based on an existing DBA object

### Usage

    dba(DBA,mask, minOverlap=2,
        sampleSheet="dba_samples.csv",
        config=data.frame(RunParallel=TRUE, reportInit="DBA", DataType=DBA_DATA_GRANGES,
                          AnalysisMethod=DBA_DESEQ2, minQCth=15, fragmentSize=125,
                          bCorPlot=FALSE, th=0.05, bUsePval=FALSE),
        peakCaller="raw", peakFormat, scoreCol, bLowerScoreBetter,
        filter, skipLines=0,
        bAddCallerConsensus=FALSE,
        bRemoveM=TRUE, bRemoveRandom=TRUE,
        bSummarizedExperiment=FALSE,
        bCorPlot, attributes, dir)

### Arguments

`DBA` | existing DBA object – if present, will return a fully-constructed DBA object based on the passed one, using criteria specified in the mask and/or minOverlap parameters. If missing, will create a new DBA object based on the sampleSheet.
`mask` | logical or numerical vector indicating which peaksets to include in the resulting model if basing DBA object on an existing one. See `dba.mask`.
`minOverlap` | only include peaks in at least this many peaksets in the main binding matrix if basing DBA object on an existing one. If minOverlap is between zero and one, peak will be included from at least this proportion of peaksets.
`sampleSheet` | data frame containing sample sheet, or file name of sample sheet to load (ignored if DBA is specified). Columns names in sample sheet may include: SampleID: Identifier string for sample Tissue: Identifier string for tissue type Factor: Identifier string for factor Condition: Identifier string for condition Treatment: Identifier string for treatment Replicate: Replicate number of sample bamReads: file path for bam file containing aligned reads for ChIP sample bamControl: file path for bam file containing aligned reads for control sample ControlID: Identifier string for control sample Peaks: path for file containing peaks for sample. format determined by PeakCaller field or caller parameter PeakCaller: Identifier string for peak caller used. If Peaks is not a bed file, this will determine how the Peaks file is parsed. If missing, will use default peak caller specified in caller parameter. Possible values: “raw”: text file file; peak score is in fourth column “bed”: .bed file; peak score is in fifth column “narrow”: default peak.format: narrowPeaks file “macs”: MACS .xls file “swembl”: SWEMBL .peaks file “bayes”: bayesPeak file “peakset”: peakset written out using pv.writepeakset “fp4”: FindPeaks v4 PeakFormat: string indicating format for peak files; see PeakCaller and `dba.peakset` ScoreCol: column in peak files that contains peak scores LowerBetter: logical indicating that lower scores signify better peaks Counts: file path for externally computed read counts; see `dba.peakset` (`counts` parameter) For sample sheets loaded from a file, the accepted formats are comma-separated values (column headers, followed by one line per sample), or Excel-formatted spreadsheets (`.xls` or `.xlsx` extension). Leading and trailing white space will be removed from all values, with a warning.
`config` | data frame containing configuration options, or file name of config file to load when constructing a new DBA object from a sample sheet. NULL indicates no config file. Relevant fields include: RunParallel: logical indicating if counting and analysis operations should be run in parallel using multicore by default. DataType: default class for peaks and reports (DBA_DATA_GRANGES, DBA_DATA_RANGEDDATA, or DBA_DATA_FRAME). ReportInit: string to append to the beginning of saved report file names. AnalysisMethod: either DBA_DESEQ2 or DBA_EDGER. bCorPlot: logical indicating that a correlation heatmap should be plotted automatically th: default threshold for reporting and plotting analysis results. bUsePval: logical, default indicating whether to use FDR (`FALSE`) or p-values (`TRUE`). minQCth: numeric, for filtering reads based on mapping quality score; only reads with a mapping qulity score gretaer than or equal to this will be counted. fragmentSize: numeric with mean fragment size. Reads will be extended to this length before counting overlaps. May be a vector of legnths, one for each sample.
`peakCaller` | if a sampleSheet is specified, the default peak caller that will be used if the `PeakCaller` column is absent.
`peakFormat` | if a sampleSheet is specified, the default peak file format that will be used if the `PeakFormat` column is absent.
`scoreCol` | if a sampleSheet is specified, the default column in the peak files that will be used for scoring if the `ScoreCol` column is absent.
`bLowerScoreBetter` | if a sampleSheet is specified, the sort order for peak scores if the `LowerBetter` column is absent.
`filter` | if a sampleSheet is specified, a filter value if the `Filter` column is absent. Peaks with scores lower than this value (or higher if `bLowerScoreBetter` or `LowerBetter` is TRUE) will be removed.
`skipLines` | if a sampleSheet is specified, the number of lines (ie header lines) at the beginning of each peak file to skip.
`bAddCallerConsensus` | add a consensus peakset for each sample with more than one peakset (i.e. different peak callers) when constructing a new DBA object from a sample sheet.
`bRemoveM` | logical indicating whether to remove peaks on chrM (mitochondria) when constructing a new DBA object from a sample sheet.
`bRemoveRandom` | logical indicating whether to remove peaks on chrN_random when constructing a new DBA object from a sample sheet.
`bSummarizedExperiment` | logical indicating whether to return resulting object as a `SummarizedExperiment`.
`bCorPlot` | logical indicating that a correlation heatmap should be plotted before returning. If `DBA` is `NULL` (a new DBA object is being created), and `bCorPlot` is missing, then this will take the default value (`FALSE`). However if `DBA` is `NULL` (a new DBA object is being created), and `bCorPlot` is specified, then the specified value will become the default value of `bCorPlot` for the resultant `DBA` object.
`attributes` | vector of attributes to use subsequently as defaults when generating labels in plotting functions: DBA_ID DBA_TISSUE DBA_FACTOR DBA_CONDITION DBA_REPLICATE DBA_CONSENSUS DBA_CALLER DBA_CONTROL
`dir` | Directory path. If supplied, files referenced in the `sampleSheet` will have this path prepended. Applies to `PeakFiles`, `bamReads`, and `bamControl`, if present. If `sampleSheet` is a filepath, this will prepended to that as well.

### Details

MODE: Construct a new DBA object from a samplesheet:

dba(sampleSheet, config, bAddCallerConsensus, bRemoveM, bRemoveRandom, attributes)

MODE: Construct a DBA object based on an existing one:

dba(DBA, mask, attributes)

MODE: Convert a DBA object to a SummarizedExperiment object:

dba(DBA, bSummarizedExperiment=TRUE)

### Value

DBA object

### Author(s)

Rory Stark and Gordon Brown

### See Also

`dba.peakset`, `dba.show`

### Examples

    # Create DBA object from a samplesheet
    ## Not run:
    basedir <- system.file("extra", package="DiffBind")
    tamoxifen <- dba(sampleSheet="tamoxifen.csv", dir=basedir)
    tamoxifen

    tamoxifen <- dba(sampleSheet="tamoxifen_allfields.csv")
    tamoxifen

    tamoxifen <- dba(sampleSheet="tamoxifen_allfields.csv",config="config.csv")
    tamoxifen

    ## End(Not run)

    #Create a DBA object with a subset of samples
    data(tamoxifen_peaks)
    Responsive <- dba(tamoxifen,tamoxifen$masks$Responsive)
    Responsive

    # change peak caller but leave peak format the same
    basedir <- system.file("extra", package="DiffBind")
    tamoxifen <- dba(sampleSheet="tamoxifen.csv", dir=basedir,
                     peakCaller="macs", peakFormat="raw", scoreCol=5 )
    dba.show(tamoxifen, attributes=c(DBA_TISSUE,DBA_CONDITION,DBA_REPLICATE,DBA_CALLER))

    # Convert DBA object to SummarizedExperiment
    data(tamoxifen_counts)
    sset <- dba(tamoxifen,bSummarizedExperiment=TRUE)
    sset

[Package DiffBind version 2.14.0 Index]