Master

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: jDMRgrid
 Type: Package
-Title: A heuristic DMR caller for large-scale WGBS data
-Version: 0.2.1
+Title: A heuristic DMR caller for large-scale WGBS data using grid approach
+Version: 0.2.4
 Authors@R: c(
-    person("Robert", "Piecyk", email = "robert.s.piecyk@gmail.com", role = c("cre","aut"), comment=c(ORCID="0000-0002-7962-2907")),
-    person("Rashmi", "Hazarika", email = "hazarika.rr@gmail.com", role = "aut"),
-    person("Yadollah", "Shahryary Dizaji", email = "shahryary@gmail.com", role = "aut"),
-    person("Frank", "Johannes", email = "frank@jlab.org", role = "aut"))
+    person(given = c("Robert", "Stefan"), family = "Piecyk", email = "robert.s.piecyk@gmail.com", role = c("cre","aut"), comment=c(ORCID="0000-0002-7962-2907")),
+    person(given = c("Rashmi", "Rekha"), family = "Hazarika", email = "hazarika.rr@gmail.com", role = "aut"),
+    person(given = "Yadollah", family = c("Shahryary", "Dizaji"), email = "shahryary@gmail.com", role = "aut"),
+    person(given = "Frank", family = "Johannes", email = "frank@jlab.org", role = "aut"))
 Description: jDMRgrid is a component of the jDMR toolkit, an essential tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in large-scale epigenomic studies involving population-level analyses and control/treatment experiments. 
     Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. 
     It determines methylation state calls for each individual sliding window based on a Hidden Markov Model (HMM) approach. 
@@ -17,7 +17,7 @@ Encoding: UTF-8
 LazyData: false
 LazyLoad: yes
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.0.0)
 Imports: 
     ape (>= 5.6.3),
     GenomicRanges (>= 1.38.0),
@@ -52,6 +52,6 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 biocViews: Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, HiddenMarkovModel
-URL: https://github.com/robert-piecyk/jDMRgrid
-BugReports: https://github.com/robert-piecyk/jDMRgrid
+URL: https://github.com/jlab-code/jDMRgrid
+BugReports: https://github.com/jlab-code/jDMRgrid
 Config/testthat/edition: 3

NAMESPACE

@@ -1,25 +1,12 @@
-export(annotate)
 export(annotateDMRs)
 export(filterDMRmatrix)
 export(filterEpiMAF)
 export(filterReplicateConsensus)
-export(gff3.in)
-export(gff3.out)
 export(makeDMRmatrix)
-export(floorDec)
 export(context.specific.DMRs)
-export(extract.context.DMRs)
-export(statusStringCheck)
-export(binGenome)
-export(split.groups)
-export(merge.bins)
-export(merge_cols)
+export(splitGroups)
 export(runjDMRgrid)
-export(makeRegionsImpute)
-export(modifiedExportMethylome)
-export(modified.estimateTransDist)
-export(makeMethimpute)
-
+export(makeMethimpute_foreach)
 import(ggplot2)
 import(utils)
 import(future)
@@ -29,6 +16,7 @@ import(biocViews)
 import(future.apply)
 import(foreach)
 importFrom(GenomicRanges,GRanges)
+importFrom(foreach, "%dopar%")
 importFrom(GenomicRanges,slidingWindows)
 importFrom(GenomicRanges,findOverlaps)
 importFrom(GenomicRanges,intersect)
@@ -58,7 +46,7 @@ importFrom(stats,coefficients)
 importFrom(stats,na.omit)
 importFrom(stats,start)
 importFrom(stats,end)
-
+importFrom(foreach, "%dopar%")
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace_all)
 importFrom(tidyr,separate)
@@ -73,7 +61,7 @@ importFrom(GenomicRanges,findOverlaps)
 importFrom(IRanges,CharacterList)
 importFrom(IRanges,ranges)
 importFrom(stats,aggregate)
-
+importFrom(Biostrings,readDNAStringSet)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
 importFrom(S4Vectors,elementMetadata)
@@ -84,11 +72,14 @@ importFrom(S4Vectors,"elementMetadata<-")
 importFrom(S4Vectors,values)
 importFrom(Biostrings,type)
 importFrom(ape,read.gff)
+importFrom(methimpute,importBismark)
+importFrom(methimpute,extractCytosinesFromFASTA)
+importFrom(methimpute,inflateMethylome)
 importFrom(data.table,uniqueN)
 importFrom(stats,ecdf)
 importFrom(stats,quantile)
 importFrom(R.utils,withTimeout)
 importFrom(methods,as)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
-importFrom(rlang,".data")
+importFrom(rlang,".data")

NEWS

@@ -1,4 +1,18 @@
-# jDMRgrid 0.2.1
+# jDMRgrid 0.2.4
+
+Changes in version 0.2.4 (2023-10-30)
+* jDMRgrid accepts Bismark CX reports (together with FASTA file; used in Bismark analysis)
+* fixed errors for R v4.0 and up
+
+Changes in version 0.2.3 (2023-10-24)
+* New form of samplefile: samplelist (DataFrame needs to supplied directly)
+* Meeting BiocCheck and R CMD check requirements
+* Updated manuals for functions and intermediate datasets to run examples for single files
+* Updated vignette
+* Functions and package meeting good coding practices
+* Faster filterDMRmatrix and findinig context specific DMRs
+* Errors were corrected
+
 
 Changes in version 0.2.2 (2023-10-19)
 * KISS & DRY code implementation