Merge pull request #41 from sartorlab/Bioc_3_10

Pull Bioc_3_10 into master for Bioconductor submission

.Rbuildignore

@@ -1,8 +1,7 @@
-^Meta$
-^doc$
+^README\.md$
 ^\.travis\.yml$
-^.*\.git$
+^\.git$
+^\.gitignore$
 ^data-raw$
-README\.md
-^\.Rprofile$
-^benchmarks$
+^doc$
+^Meta$

.gitignore

@@ -1,2 +1,3 @@
+inst/doc
+doc
 Meta
-.DS_Store

.travis.yml

@@ -1,24 +1,9 @@
-# Sample .travis.yml for R projects
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-language: r
+language: R
 r:
-  - 3.4
-sudo: false
+    - release
+    - devel
 cache: packages
-bioc_required: true
-warnings_are_errors: false
-
-env:
- global:
-   - CRAN: http://cran.rstudio.com
-
-r_github_packages:
-  - jimhester/covr
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
-
 after_success:
-  - Rscript -e 'covr::coveralls()'
+    - Rscript -e 'covr::coveralls()'

DESCRIPTION

@@ -1,43 +1,49 @@
 Package: methylSig
-Type: Package
-Title: a whole genome DNA methylation analysis pipeline
-Version: 0.5.2
-Date: 2019-01-26
-Authors@R: c(
-    person("Yongseok", "Park", email = "[email protected]", role = c("aut")),
-    person("Raymond G.", "Cavalcante", email = "[email protected]", role = c("aut", "cre")))
-Description: MethylSig is a method for testing for differentially methylated
-    cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (bis-
-    seq) or reduced representation bisulfite sequencing (RRBS) experiments.
-    MethylSig uses a beta binomial model to test for significant differences
-    between groups of samples. Several options exist for either site-specific
-    or sliding window tests, combining strands, and for variance estimation.
-    It allows annotating the resulting regions to multiple genome features, and
-    visualizing the results for chosen genomic regions along with supporting genomic
-    information.
-biocViews: DNAMethylation, DifferentialMethylation, Epigenetics, Regression, MethylSeq
-License: GPL-3
-BugReports: https://github.com/sartorlab/methylSig/issues
+Title: MethylSig: Differential Methylation Testing for WGBS and RRBS Data
+Version: 0.99.0
+Date: 2020-03-20
+Authors@R:
+    c(person(given = "Yongseok",
+             family = "Park",
+             role = "aut",
+             email = "[email protected]"),
+      person(given = "Raymond G.",
+             family = "Cavalcante",
+             role = c("aut", "cre"),
+             email = "[email protected]"))
+Description: MethylSig is a package for testing for
+    differentially methylated cytosines (DMCs) or regions (DMRs) in
+    whole-genome bisulfite sequencing (WGBS) or reduced representation
+    bisulfite sequencing (RRBS) experiments.  MethylSig uses a beta
+    binomial model to test for significant differences between groups of
+    samples. Several options exist for either site-specific or sliding
+    window tests, and variance estimation.
 Depends:
-    R (>= 3.4)
+    R (>= 3.6)
 Imports:
-    annotatr,
-    BiocGenerics,
-    boot,
     bsseq,
     DelayedArray,
+    DelayedMatrixStats,
     DSS,
+    IRanges,
     GenomeInfoDb,
     GenomicRanges,
     methods,
     parallel,
+    stats,
     S4Vectors
 Suggests:
     BiocStyle,
-    gplots,
-    testthat,
+    bsseqData,
     knitr,
     rmarkdown,
-    rtracklayer
+    testthat (>= 2.1.0),
+    covr
+License: GPL-3
+BugReports: https://github.com/sartorlab/methylSig/issues
+biocViews: DNAMethylation, DifferentialMethylation, Epigenetics,
+    Regression, MethylSeq
+Encoding: UTF-8
+LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2

NAMESPACE

@@ -1,21 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
-export(binomialDiffCalc)
-export(methylSig.tfbsEnrichTest)
-export(methylSigAnnotation)
-export(methylSigCalc)
-export(methylSigDSS)
-export(methylSigReadData)
-export(methylSigTile)
-export(methylSig_weightFunc)
-import(BiocGenerics)
+export(diff_binomial)
+export(diff_dss_fit)
+export(diff_dss_test)
+export(diff_methylsig)
+export(filter_loci_by_coverage)
+export(filter_loci_by_group_coverage)
+export(filter_loci_by_location)
+export(tile_by_regions)
+export(tile_by_windows)
 import(DSS)
 import(DelayedArray)
+import(DelayedMatrixStats)
 import(GenomeInfoDb)
 import(GenomicRanges)
+import(IRanges)
 import(S4Vectors)
-import(annotatr)
 import(bsseq)
-import(methods)
-importFrom(boot,corr)
-importFrom(parallel,mclapply)
+import(parallel)
+importFrom(methods,is)
+importFrom(stats,as.formula)
+importFrom(stats,formula)
+importFrom(stats,p.adjust)
+importFrom(stats,pchisq)
+importFrom(stats,pt)

NEWS

@@ -0,0 +1,16 @@
+Changes in 0.99.0 (2020-03-23)
++ Refactor functions and workflow from pre-0.99.0 releases
+  o methylSigReadData() replaced with the functions:
+    o bsseq::read.bismark()
+    o filter_loci_by_coverage()
+    o filter_loci_by_location()
+  o methylSigTile() replaced with the functions:
+    o tile_by_regions()
+    o tile_by_windows()
+  o Differential testing should be preceded with:
+    o filter_loci_by_group_coverage()
+  o binomialDiffCalc() is replaced by diff_binomial()
+  o methylSigCalc() is replaced by diff_methylSig()
+  o methylSigDSS() is replaced by diff_dss_fit() and diff_dss_test()
++ See "Using methylSig" vignette for full example.
++ See "Updating methylSig Code" vignette for how to retrofit pre-0.99.0 code.