dba.show: List attributes of peaksets of contrasts associated with a...
In DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	dba.show(DBA, mask, attributes, bContrasts=FALSE, bDesign=FALSE, th=DBA$config$th)

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.

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)

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

Rory Stark

dba, dba.peakset, dba.contrast. dba.analyze

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