Constant variables used in DiffBind package

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Description

Constant variables used in DiffBind package

Usage

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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.

Note

Variables with ALL CAP names are used as constants within DiffBind.

Author(s)

Rory Stark