DiffBind – DBA global constant variables {DiffBind} | R Documentation |
Constant variables used in DiffBind package
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
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_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: |
DBA_ALL_BLOCK |
report on block results for both analysis methods: |
DBA_ALL_METHODS_BLOCK |
report on block results for all analysis methods, both blocked and unblocked: |
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 |
DBA_DATA_DBAOBJECT |
Return a result-based DBA object from |
Variables with ALL CAP names are used as constants within DiffBind.
Rory Stark