dba.show {DiffBind} | R Documentation

## List attributes of peaksets of contrasts associated with a DBA object

### Description

Returns attributes of peaksets and/or contrasts associated with a DBA object.

### Usage

    dba.show(DBA, mask, attributes, bContrasts=FALSE, bDesign=FALSE,
             th=DBA$config$th)

### Arguments

`DBA` | DBA object

`mask` | mask of peaksets for which to get attributes (used when obtaining peakset attributes, i.e. `bContrasts=FALSE`).
`attributes` | attribute or vector of attributes to retrieve. Number of intervals is always shown. Used when obtaining peakset attributes, i.e. `bContrasts=FALSE`. Values: `DBA_ID` `DBA_TISSUE` `DBA_FACTOR` `DBA_CONDITION` `DBA_TREATMENT` `DBA_REPLICATE` `DBA_CONSENSUS` `DBA_CALLER` `DBA_CONTROL` `DBA_READS` `DBA_INTERVALS` `DBA_FRIP`
`bContrasts` | logical indicating whether peaksets or contrast attributes are to be retrieved. `TRUE` retrieves a dataframe of contrast information instead of peakset attributes. If no contrasts are set, returns possible contrasts. See `dba.contrast`.
`bDesign` | logical indicating whether the model design should be returned, if present. `bContrasts` must be `FALSE` for this parameter to be used.
`th` | if `bContrasts` is `TRUE`, then `th` is used as the threshold for determining how many significant sites there are for each contrast. Only relevant when obtaining contrast attributes (`bContrasts=TRUE`) and `dba.analyze` has been run.

### Details

MODE: Return attributes of peaksets associated with a DBA object:

`dba.show(DBA, mask, attributes)`

MODE: Return contrasts associated with a DBA object:

`dba.show(DBA,bContrasts=TRUE, th)`

MODE: Return design associated with a DBA object:

`dba.show(DBA,bDesign=TRUE)`

### Value

dataframe with peakset attributes.

If `bContrasts == FALSE`, each row represents a peakset, and each column is an attributes, with the final column, Intervals, indicating how many sites there are in the peakset.

If `bContrasts == TRUE`, each row represent a contrast, with the following columns:

``Group1`` | Label for first group of contrast
``Members1`` | Number of samples in first group of contrast
``Group2`` | Label for first group of contrast
``Members3`` | Number of samples in first group of contrast

if `dba.analyze` has been successfully run, there there will be up to four more columns showing the number of significant differentially bound (DB) sites identified for

``DB.edgeR`` | Number of significantly differentially bound sites identified using edgeR
``DB.DESeq`` | Number of significantly differentially bound sites identified using DESeq
``DB.edgeR.block`` | Number of significantly differentially bound sites identified for blocking analysis using edgeR
``DB.DESeq.block`` | Number of significantly differentially bound sites identified for blocking analysis using DESeq

### Author(s)

Rory Stark

### See Also

`dba`, `dba.peakset`, `dba.contrast` `dba.analyze`, `DBA.config`.

### Examples

    data(tamoxifen_peaks)
    dba.show(tamoxifen)
    dba.show(tamoxifen,tamoxifen$masks$Responsive)
    dba.show(tamoxifen,attributes=c(DBA_TISSUE,DBA_REPLICATE,DBA_CONDITION))

    data(tamoxifen_analysis)
    dba.show(tamoxifen,bContrasts=TRUE)

    #alternatively:
    data(tamoxifen_analysis)
    tamoxifen
    tamoxifen$config$th <- .01
    tamoxifen

[Package DiffBind version 3.2.7 Index]