dba.show {DiffBind} | R Documentation |
Returns attributes of peaksets and/or contrasts associated with a DBA object.
dba.show(DBA, mask, attributes, bContrasts=FALSE, th=DBA$config$th, bUsePval=DBA$config$bUsePval)
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. TRUE retrieves a dataframe of contrast information instead of peakset attributes. If no contrasts are set, returns possible contrasts. See |
th |
if |
bUsePval |
logical indicating that p-values will be used (along with |
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)
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_counts) tamoxifen <- dba.contrast(tamoxifen) dba.show(tamoxifen,bContrasts=TRUE) #alternatively: tamoxifen tamoxifen$config$th <- .05 tamoxifen