dba.show {DiffBind} | R Documentation |
Returns attributes of peaksets and/or contrasts associated with a DBA object.
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. |
attributes |
attribute or vector of attributes to retrieve.
Number of intervals is always shown.
Used when obtaining peakset attributes, i.e. |
bContrasts |
logical indicating whether peaksets or contrast attributes are to be retrieved.
|
bDesign |
logical indicating whether the model design should be returned, if present.
|
th |
if |
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:
|
Label for first group of contrast |
|
Number of samples in first group of contrast |
|
Label for first group of contrast |
|
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
|
Number of significantly differentially bound sites identified using edgeR |
|
Number of significantly differentially bound sites identified using DESeq |
|
Number of significantly differentially bound sites identified for blocking analysis using edgeR |
|
Number of significantly differentially bound sites identified for blocking analysis using DESeq |
Rory Stark
dba
, dba.peakset
, dba.contrast
dba.analyze
, DBA.config
.
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