rowData - DataFrame - promoterID, geneID, transcriptID, seqname, strand, promoter position, promoter activity summarized by condition, and promoter category by condition
mclapply to bplapply
Creating Promoter Annotations
preparePromoterAnnotation function
Builds promoter annotation
Compulsory arguments - species and either txdb or file ; file can be path to a GTF or a TxDb
Improved efficiency in generating annotations without parallelization (~2 mins for hg38 annotation)
Main improvements for helper functions getIntronRanks and getReducedExons
Combine 4 helper functions in annotation-data into one function to avoid repeated calls to certain helper functions which are time-expensive
To comply with Bioconductor guidelines on package size, promoter annotation is shrunk
From 4 slots to 3 slots - intronRanges, promoterIdMapping, promoterCoordinates
Metadata not necessary for running proActiv is removed
Promoter annotations for multiple genomes exported to user
hg19 / hg38
mm9 / mm10
Plotting promoter activity
plotPromoters function visualizes promoter activity across conditions with Gviz
Compulsory arguments result (summarizedExperiment object returned by proActiv), gene of interest and annotation object - either txdb or GRangesList of exonsByTranscripts ranges
Allows users to visualize promoter activity and identify instances of alternative promoter usage
Vignette
proActiv now comes with a vignette, documenting a complete step-by-step workflow in identifying active and alternative promoter usage
Includes sections:
Running proActiv
Creating promoter annotations
Identifying alternative promoter usage with DEXSeq
Visualizations of promoter activity:
plotPromoters
Promoter category proportions across conditions
Major-minor promoters by position (5' -> 3')
Major promoter activity vs. gene expression
t-SNE plot with active promoters
Tests
Include units tests for:
annotation-data.R / annotation-data-helper.R
junction-read-count.R
estimate-promoter-activity.R
proActiv.R
Reexports
Reexport certain imported functions from other packages loaded with proActiv namespace - primarily for use in vignette (e.g. getters for summarizedExperiment rowData, assays...)
extdata
Vignette directory
Annotations directory
Contains genomic annotation data to be used in the vignette. including
gencode.v34.annotations subsetted to chromosome 22 (gtf, sqlite)
RAP1GAP data for visualization with plotPromoters
Junctions directory
Contains STAR junction files from SGNEx data (3 x A549, 3 x HepG2)
Testdata directory
data used for testing (incl. subsetted bam files, star and tophat2 junction files, and promoter annotations)
Calculating Promoter Activity
proActiv
functionproActiv
calls the functions to calculate junctions counts and estimate promoter activityfiles
and promoter annotation objectpromoterAnnotation
fileLabels
andncores
;genome
argument is required if input is a BAM filecondition
can be supplied - proActiv will summarize promoter counts and activity across conditions if this is the casepromoterCounts
,normalizedPromoterCounts
,absolutePromoterActivity
,relativePromoterActivity
geneExpression
mclapply
tobplapply
Creating Promoter Annotations
preparePromoterAnnotation
functionspecies
and eithertxdb
orfile
;file
can be path to a GTF or a TxDbgetIntronRanks
andgetReducedExons
annotation-data
into one function to avoid repeated calls to certain helper functions which are time-expensiveintronRanges
,promoterIdMapping
,promoterCoordinates
Promoter annotations for multiple genomes exported to user
Plotting promoter activity
plotPromoters
function visualizes promoter activity across conditions with Gvizresult
(summarizedExperiment object returned byproActiv
),gene
of interest and annotation object - eithertxdb
or GRangesList of exonsByTranscriptsranges
Vignette
plotPromoters
Tests
annotation-data.R
/annotation-data-helper.R
junction-read-count.R
estimate-promoter-activity.R
proActiv.R
Reexports
rowData
,assays
...)extdata
plotPromoters