DiffBind (version 2.0.2)

DiffBind -- DBA global constant variables: Constant variables used in DiffBind package

Description

Constant variables used in DiffBind package

Usage

DBA_ID DBA_FACTOR DBA_TISSUE DBA_CONDITION DBA_TREATMENT DBA_REPLICATE DBA_CALLER DBA_CONSENSUS DBA_CONTROL DBA_ALL_ATTRIBUTES
DBA_INTERVALS DBA_FRIP
DBA_GROUP
DBA_OLAP_PEAKS DBA_OLAP_ALL DBA_OLAP_RATE
DBA_COR DBA_OLAP DBA_INALL
DBA_SCORE_READS DBA_SCORE_READS_MINUS DBA_SCORE_READS_FOLD DBA_SCORE_RPKM DBA_SCORE_RPKM_FOLD DBA_SCORE_TMM_READS_FULL DBA_SCORE_TMM_READS_EFFECTIVE DBA_SCORE_TMM_MINUS_FULL DBA_SCORE_TMM_MINUS_EFFECTIVE DBA_SCORE_TMM_READS_FULL_CPM DBA_SCORE_TMM_READS_EFFECTIVE_CPM DBA_SCORE_TMM_MINUS_FULL_CPM DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM DBA_SCORE_SUMMIT DBA_SCORE_SUMMIT_ADJ DBA_SCORE_SUMMIT_POS
DBA_READS_DEFAULT DBA_READS_BAM DBA_READS_BED
DBA_EDGER DBA_DESEQ DBA_DESEQ2 DBA_EDGER_BLOCK DBA_DESEQ_BLOCK DBA_DESEQ2_BLOCK DBA_EDGER_CLASSIC DBA_DESEQ_CLASSIC DBA_EDGER_GLM DBA_DESEQ_GLM DBA_ALL_METHODS DBA_ALL_BLOCK DBA_ALL_METHODS_BLOCK
DBA_DATA_FRAME DBA_DATA_GRANGES DBA_DATA_RANGEDDATA DBA_DATA_SUMMARIZED_EXPERIMENT DBA_DATA_DBAOBJECT

Arguments

DBA_ID
DBA peakset metadata: Peakset ID
DBA_FACTOR
DBA peakset metadata: Factor
DBA_TISSUE
DBA peakset metadata: Tissue
DBA_CONDITION
DBA peakset metadata: Condition
DBA_TREATMENT
DBA peakset metadata: Treatment
DBA_REPLICATE
DBA peakset metadata: Replicate
DBA_CALLER
DBA peakset metadata: Peak Caller
DBA_CONSENSUS
DBA peakset metadata: Is this a consensus peakset?
DBA_CONTROL
DBA peakset metadata: ID of Control sample
DBA_ALL_ATTRIBUTES
DBA peakset metadata: all attributes that can be used in certain plot labels (cf dba.plotVenn), equivalent to c(DBA_ID, DBA_TISSUE, DBA_FACTOR, DBA_CONDITION,DBA_TREATMENT, DBA_REPLICATE, DBA_CALLER)
DBA_INTERVALS
DBA peakset metadata: Number of intervals in peakset
DBA_FRIP
DBA peakset metadata: Fraction of Reads in Peaks (number of reads in intervals divided by total number of reads in library)
DBA_GROUP
DBA peakset metadata: color PCA plot using contras groups
DBA_OLAP_PEAKS
dba.overlap mode: return overlapping/unique peaksets
DBA_OLAP_ALL
dba.overlap mode: return report of correlations/overlaps for each pair of samples
DBA_OLAP_RATE
dba.overlap mode: return overlap rates
DBA_COR
When plotting a heatmap from an overlap record, use the correlation value.
DBA_OLAP
When plotting a heatmap from an overlap record, use the percentage overlap value.
DBA_INALL
When plotting a heatmap from an overlap record, use the number of peaks in common to both samples.
DBA_SCORE_READS
dba.count score is number of reads in ChIP
DBA_SCORE_READS_FOLD
dba.count score is number of reads in ChIP divided by number of reads in Control
DBA_SCORE_READS_MINUS
dba.count score is number of reads in ChIP minus number of reads in Control
DBA_SCORE_RPKM
dba.count score is RPKM of ChIP
DBA_SCORE_RPKM_FOLD
dba.count score is RPKM of ChIP divided by RPKM of Control
DBA_SCORE_TMM_READS_FULL
dba.count score is TMM normalized (using edgeR), using ChIP read counts and Full Library size
DBA_SCORE_TMM_READS_EFFECTIVE
dba.count score is TMM normalized (using edgeR), using ChIP read counts and Effective Library size
DBA_SCORE_TMM_MINUS_FULL
dba.count score is TMM normalized (using edgeR), using ChIP read counts minus Control read counts and Full Library size
DBA_SCORE_TMM_MINUS_EFFECTIVE
dba.count score is TMM normalized (using edgeR), using ChIP read counts minus Control read counts and Effective Library size
DBA_SCORE_TMM_READS_FULL_CPM
dba.count score is TMM normalized (using edgeR), using ChIP read counts and Full Library size, reported in counts-per-million.
DBA_SCORE_TMM_READS_EFFECTIVE_CPM
dba.count score is TMM normalized (using edgeR), using ChIP read counts and Effective Library size, reported in counts-per-million.
DBA_SCORE_TMM_MINUS_FULL_CPM
dba.count score is TMM normalized (using edgeR), using ChIP read counts minus Control read counts and Full Library size, reported in counts-per-million.
DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM
dba.count score is TMM normalized (using edgeR), using ChIP read counts minus Control read counts and Effective Library size, reported in counts-per-million.
DBA_SCORE_SUMMIT
dba.count score is summit height (highest pile-up).
DBA_SCORE_SUMMIT_ADJ
dba.count score is summit height (highest pile-up), adjusted for library size.
DBA_SCORE_SUMMIT_POS
dba.count score is summit location (position of highest pile-up).
DBA_READS_DEFAULT
When counting read files, use the file extension to determine the file type.
DBA_READS_BAM
When counting read files, assume the file type is BAM, regardless of the file extension.
DBA_READS_BED
When counting read files, assume the file type is BED (or zipped BED), regardless of the file extension.
DBA_EDGER
differential analysis method: edgeR (default: DBA_EDGER_GLM)
DBA_DESEQ2
differential analysis method: DESeq2 (using a single-factor GLM)
DBA_EDGER_BLOCK
differential analysis method: edgeR with blocking factors (GLM)
DBA_DESEQ2_BLOCK
differential analysis method: DESeq2 with blocking factors (GLM)
DBA_DESEQ
differential analysis method: DESeq (default: DBA_DESEQ_CLASSIC)
DBA_DESEQ_BLOCK
differential analysis method: DESeq with blocking factors (GLM)
DBA_EDGER_CLASSIC
differential analysis method: "classic" edgeR for two-group comparisons
DBA_DESEQ_CLASSIC
differential analysis method: "classic" DESeq for two-group comparisons
DBA_EDGER_GLM
differential analysis method: use GLM in edgeR for two-group comparisons
DBA_DESEQ_GLM
differential analysis method: use GLM in DESeq for two-group comparisons
DBA_ALL_METHODS
use both analysis methods: c(DBA_EDGER, DBA_DESEQ2)
DBA_ALL_BLOCK
report on block results for both analysis methods: c(DBA_EDGER_BLOCK, DBA_DESEQ2_BLOCK)
DBA_ALL_METHODS_BLOCK
report on block results for all analysis methods, both blocked and unblocked: c(DBA_ALL_METHODS, DBA_ALL_BLOCK)
DBA_DATA_GRANGES
Use GRanges class for peaksets and reports. This is the default (DBA$config$DataType = DBA_DATA_GRANGES).
DBA_DATA_RANGEDDATA
Use RangedData class for peaksets and reports. Can be set as default (DBA$config$DataType = DBA_DATA_RANGEDDATA).
DBA_DATA_FRAME
Use data.frame class for peaksets and reports. Can be set as default (DBA$config$DataType = DBA_DATA_FRAME).
DBA_DATA_SUMMARIZED_EXPERIMENT
Return report as a SummarizedExperiment.
DBA_DATA_DBAOBJECT
Return a result-based DBA object from dba.plotVenn.