In Bioconductor/VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

5/6/2019, pre-submission todo: - fix "FIXME" tags in testthat.

07/02/2018

• to pass check() and BiocCheck::check(). -- no "inst/doc/VariantExperiment.html" detected.

• adding new stats functions: -- BCF2VE, VCF2VE (vcf.fn argument?) -- only keep VCF2VE now!

• add examples for:
• VCF2VE -- done!
• makeSEFromGDS -- done!
• showAvailable() -- done!

• ...

• vignette. -- done!

• documentation for arguments. -- done!
• gdsfile() return an atomic vector. (currently using vapply). -- done!
• construct a valid empty VE object, by VariantExperiment(). -- done!
• disable the "gdsfile()<-" setter function. -- done!
• consistent argument values. -- done!

• "makeSummarizedExperimentFromVCF(info.import)" with "makeSummarizedExperimentFromGDS(info.columns)". Make default as "NULL" to import all info, and when "character(0)", import nothing.

• renaming: save/loadGDSSummarizedExperiment ==> save/loadVariantExperiment -- done! keep "makeSummarizedExperimentFromGDS" -- done! VCF2VE ==> makeSummarizedExperimentFromVCF ?? -- done!

• bugs

• ?VariantExperiment-methods (last line). -- done!

• vignette not generating in inst/doc. -- done! -- DESCRIPTION: VignetteBuilder: knitr Suggests: knitr

• add example ve.gds, ve.rd file under "inst/extdata". ??

• reactivate the "gdsfile<-" setter function... ??

• bugs: -- workaround fixed! -- devtools::document(), first time document() reserves SeqVarTools::titv() methods/functions, second time document() lost all methods for "SeqVarGDSClass"... ## unable to find an inherited method for function ‘meanBySample’ for signature ‘"SeqVarGDSClass"’ ## FIX workaround fix: library(SeqVarGDSClass) when developing. Only problem with "devtools", will not affect the check().

-- question for martin: 1. VariantExperiment() constructor, should we copy all argument documentations from SummarizedExperiment?

1. next phase:
2. add more sample related stats functions. (need real data)
3. add block processing, and apply functions.
4. connection with VariantAnnotation (collapsedVCF? in memory)?
5. for annotation: AnnotationHub? (ensemblVEP, VariantFiltering..., dbsnp pkgs).
6. filtering, using rowRanges, overlap...
7. sample.annotation related stat analysis: mendelian errors? (use family info, test!!) - next phase!
8. association test associated analysis? -- next phase!
9. gds attributes to save in metadata? -- header info. no need to save vcf file now... wait until connecting to VariantAnnotation. -- sample.order / snp.order, VCF version, ... not super important for VE analysis.

Vignette

1. introduction.
2. installation.
3. BackGround
4. GDSArray
5. DelayedDataFrame
6. VariantExperiment-package
7. VariantExperiment-class (class, setters and getters)
8. VariantExperiment-methods (VCF2VE, titv... vcf related.)

9. common manipulations... (subsetting, save new VE file, load VE file, ... ) FIXME: slot setter? gdsfile() <- FIXME: saveGDSSE(dir="my_gds_se") or use tempfile() here? -- use "tempdir()" in vignette.

10. sessionInfo

Bioconductor/VariantExperiment documentation built on April 20, 2024, 3:02 p.m.