DiffBind (version 2.0.2)

dba.show: 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.

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

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)

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

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