Closed jleechung closed 4 years ago
* Add Windows parallelization in `getReducedExonRanges` (`annotation-data-helper.R`) Detects user OS and calls `BiocParallel` if OS is Windows. Scales well (runtime approximately halved with number of cores = 2) * Add BAM file usage for `calculateJunctionReadCounts` (`junction-read-count.R`) Reads BAM file using `GenomicAlignments::readGAlignments` and `summarizeJunctions`. Extra argument 'genome' is required to infer strand of junctions for downstream analysis ( i.e., to prevent ambiguous junctions returned when overlapped with `intronRanges`). Removes BAM files immediately after processing and calls garbage collection to free up memory. Examples for `calculateJunctionReadCounts` and `calculatePromoterReadCounts` with BAM usage added * Add Windows parallelization for `calculatePromoterReadCounts` (`junction-read-count.R`) Detects user OS and calls `BiocParallel` if OS is Windows. Scales for large number of input junction files * Allow for unspecified file labels by creating labels if user does not provide labels argument in `calculatePromoterReadCounts` (`junction-read-count.R`) If labels unprovided, simply creates labels 's1', 's2', ... * Wrapper function `proActiv.R` Takes in minimally arguments `promoterAnnotationData`, `junctionFilePaths` and `junctionType` (and `genome` if input is a BAM file), returning a `summarizedExperiment` object giving promoter counts and activity, with promoter-gene mapping (stored as row data) and gene expression (stored as column data)
Thanks @jleechung , really a lot of very helpful additions. I made some comments regarding some of the code, please have a look.
Add Windows parallelization in
getReducedExonRanges
(annotation-data-helper.R
) Detects user OS and callsBiocParallel
if OS is Windows. Scales well (runtime approximately halved with number of cores = 2)Add BAM file usage for
calculateJunctionReadCounts
(junction-read-count.R
) Reads BAM file usingGenomicAlignments::readGAlignments
andsummarizeJunctions
. Extra argument 'genome' is required to infer strand of junctions for downstream analysis ( i.e., to prevent ambiguous junctions returned when overlapped withintronRanges
). Removes BAM files immediately after processing and calls garbage collection to free up memory. Examples forcalculateJunctionReadCounts
andcalculatePromoterReadCounts
with BAM usage addedAdd Windows parallelization for
calculatePromoterReadCounts
(junction-read-count.R
) Detects user OS and callsBiocParallel
if OS is Windows. Scales for large number of input junction filesAllow for unspecified file labels by creating labels if user does not provide labels argument in
calculatePromoterReadCounts
(junction-read-count.R
) If labels unprovided, simply creates labels 's1', 's2', ...Wrapper function
proActiv.R
Takes in minimally argumentspromoterAnnotationData
,junctionFilePaths
andjunctionType
(andgenome
if input is a BAM file), returning asummarizedExperiment
object giving promoter counts and activity, with promoter-gene mapping (stored as row data) and gene expression (stored as column data)