DBA object methods {DiffBind} | R Documentation

## Standard S3 methods for DBA object

### Description

Standard S3 methods for DBA object.

### Usage

    ## S3 method for class 'DBA'
    print(x, ...)
    ## S3 method for class 'DBA'
    summary(object, ...)
    ## S3 method for class 'DBA'
    plot(x, ...)

### Arguments

`x` | DBA object
`object` | DBA object
`...` | Arguments passed on to parent methods

### Details

S3 methods for DBA object from the `DiffBind` package.

DBA objects are usually constructed using the `dba` function.

There are a number of internal parameters that can be set, and defaults overridden, by setting `DBA$config` options:

- `DBA$config$AnalysisMethod:` either `DBA_DESEQ2` or `DBA_EDGER`.

- `DBA$config$th:` default threshold for reporting and plotting analysis results.

- `DBA$config$DataType:` default class for peaks and reports (`DBA_DATA_GRANGES, DBA_DATA_RANGEDDATA, or DBA_DATA_FRAME`).

- `DBA$config$RunParallel:` logical indicating if counting and analysis operations should be run in parallel using multicore by default.

- `DBA$config$cores:` number of cores to use when performing multi-core parallel processing.

- `DBA$config$minQCth:` numeric, for filtering reads based on mapping quality score; only reads with a mapping quality score greater than or equal to this will be counted.

- `DBA$config$fragmentSize:` numeric indicating mean fragment size for single-end counting. Reads will be extended to this length before counting overlaps. May be a vector of lengths, one for each sample.

- `DBA$config$bCorPlot:` logical indicating that a correlation heatmap should be plotted automatically

- `DBA$config$ReportInit:` string to append to the beginning of saved report file names.

- `DBA$config$bUsePval:` logical, default indicating whether to use FDR (`FALSE`) or p-values (`TRUE`).

- `DBA$config$doBlacklist:` logical, whether to attempt to find and apply a blacklist if none is present when running `dba.analyze`.

- `DBA$config$doGreylist` logical, whether to attempt to generate and apply a greylist if none is present when running `dba.analyze`.

- `DBA$config$DataType` The class of object for returned reports and peaksets:

  - `DBA_DATA_GRANGES`

  - `DBA_DATA_RANGEDDATA`

  - `DBA_DATA_FRAME`

  - `DBA_DATA_SUMMARIZED_EXPERIMENT`

- `DBA$config$mergeOverlap:` The overlap (in basepairs) between peaks to merge when generating a consensus peakset. A positive valuecontrols how many basepairs peaks must overlap to be merged, while a negative value will result in non-overlapping peaks to be merged,

  If absent, the default value of `1` will result in any peaks overlapping by at least one basepair to be merged into a single interval.

- `DBA$config$design:` When calling `dba.contrast`, if `design` parameter is missing, this will be used as the value for that parameter.

- `DBA$config$edgeR$bTagwise:` `logical` indicating if `edgeR::estimateGLMTagwiseDisp` should be called when performing an `edgeR` analysis. If absent the default is `TRUE`, so setting this to `FALSE` prevents the tagwise dispersion estimate form being calculated.

- `DBA$config$DESeq2$fitType:` `logical` indicating the `fitType` to be used in `DESeq2::estimateDispersions` when performing a `DESeq2` analysis. If absent the default is `local`.

- `DBA$config$savePrefix:` When calling `dba.save` or `dba.load`, this value (if present) will override the default value for the `pre` parameter.

- `DBA$config$saveExt:` When calling `dba.save` or `dba.load`, this value (if present) will override the default value for the `ext` parameter.

- `DBA$config$greylist.pval:` pvalue cutoff to use when generating a greylist using `GreyListChIP::calcThreshold`. If missing, the default is `0.999`

- `DBA$config$saveExt:` When calling `dba.save`, this value (if present) will override the default value for the `ext` parameter.

- `DBA$config$yieldSize:` yieldSize indicating how many reads to process at one time; default is 5000000. The lower this value, the less memory will be used, but the more time it will take to complete the count operation.

- `DBA$config$intersectMode:` mode indicating which overlap algorithm to use; default is `"IntersectionNotEmpty"`

- `DBA$config$singleEnd:` `logical` indicating if reads are single end; if `NULL`, status will be automatically detected.

- `DBA$config$fragments:` `logical` indicating how unmatched reads are counted; default is `FALSE`.

- `DBA$config$scanbamparam:` `ScanBamParam` object to pass to `summarizeOverlaps`. If present, `bRemoveDuplicates` is ignored.

- `DBA$config$pp.style:` Sets `style` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$pp.nOfWindows:` Sets `nOfWindow` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$bin_size:` Sets `bin_size` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$distanceAround:` Sets `distanceAround` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$distanceUp:` Sets `distanceUp` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$distanceDown:` Sets `distanceDown` parameter for `profileplyr::BamBigwig_to_chipProfile` when calling `dba.plotProfile.`

- `DBA$config$id:` `character` string to use to replace `"ID"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$group:` `character` string to use to replace `"Group"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$tissue:` `character` string to use to replace `"Tissue"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$factor:` `character` string to use to replace `"Factor"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$condition:` `character` string to use to replace `"Condition"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$treatment:` `character` string to use to replace `"Treatment"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$replicate:` `character` string to use to replace `"Replicate"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$caller:` `character` string to use to replace `"Caller"` when displaying a `DBA` object (`dba.show`)

- `DBA$config$reads:` `character` string to use to replace `"Reads"` when displaying a `DBA` object (`dba.show`)

### Author(s)

Rory Stark

### Examples

    data(tamoxifen_peaks)
    tamoxifen
    data(tamoxifen_counts)
    tamoxifen

[Package DiffBind version 3.2.7 Index]