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!
...
vignette. -- done!
VariantExperiment()
. -- 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
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?
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.
sessionInfo
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