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,
             th=DBA$config$th, bUsePval=DBA$config$bUsePval)

### 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_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`.
`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.
`bUsePval` | logical indicating that p-values will be used (along with `th`) to determine how many significant sites there are for each contrast; if FALSE, adjusted p-values (FDR) are used. 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=T, th, bUsePval)

### 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`

### 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_counts)
    tamoxifen <- dba.contrast(tamoxifen)
    dba.show(tamoxifen,bContrasts=TRUE)

    #alternatively:
    tamoxifen
    tamoxifen$config$th <- .05
    tamoxifen

[Package DiffBind version 2.15.2 Index]