remove deprecated functions, fix bugs

GreenleafLab · Oct 12, 2017 · cddbf26 · cddbf26
1 parent 243d192
commit cddbf26
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Showing 21 changed files with 59 additions and 622 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,4 +8,5 @@
 ^.Rhistory$
 ^.RData$
 ^.gitignore$
-^.travis.yml$
+^.travis.yml$
+^_gh_pages$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: chromVAR
 Type: Package
 Title: Chromatin Variation Across Regions
-Version: 0.99.0.9999
+Version: 0.99.1
 Date: 2016-12-20
 Authors@R: c(
     person("Alicia", "Schep", email = "[email protected]", role = c("aut","cre")),
@@ -52,8 +52,6 @@ Suggests:
     rmarkdown,
     pheatmap,
     motifmatchr
-Remotes:
-    GreenleafLab/motifmatchr
 biocViews: SingleCell, Sequencing, GeneRegulation
 LazyData: TRUE
 LinkingTo: Rcpp, RcppArmadillo

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,33 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
 export(addGCBias)
-export(add_gc_bias)
 export(annotationMatches)
-export(annotation_matches)
 export(assembleKmers)
-export(assemble_kmers)
 export(chromVAR_theme)
 export(computeDeviations)
 export(computeExpectations)
 export(computeVariability)
-export(compute_deviations)
-export(compute_expectations)
-export(compute_variability)
-export(deviation_scores)
 export(deviationsCovariability)
 export(deviationsTsne)
-export(deviations_covariability)
-export(deviations_tsne)
 export(differentialDeviations)
 export(differentialVariability)
-export(differential_deviations)
-export(differential_variability)
 export(filterPeaks)
 export(filterSamples)
 export(filterSamplesPlot)
-export(filter_peaks)
-export(filter_samples)
-export(filter_samples_plot)
 export(getAnnotationCorrelation)
 export(getAnnotationSynergy)
 export(getAnnotations)
@@ -43,37 +29,14 @@ export(getSampleCorrelation)
 export(getSampleDepths)
 export(getSampleDistance)
 export(getTotalFragments)
-export(get_annotation_correlation)
-export(get_annotation_synergy)
-export(get_annotations)
-export(get_background_peaks)
-export(get_cis_groups)
-export(get_counts)
-export(get_fragments_per_peak)
-export(get_fragments_per_sample)
-export(get_jaspar_motifs)
-export(get_peaks)
-export(get_permuted_data)
-export(get_sample_correlation)
-export(get_sample_depths)
-export(get_sample_distance)
-export(get_total_fragments)
 export(makeBiasBins)
 export(makePermutedSets)
-export(make_bias_bins)
-export(make_permuted_sets)
 export(matchKmers)
-export(match_kmers)
 export(plotDeviationsTsne)
 export(plotKmerMismatch)
 export(plotVariability)
-export(plot_deviations_tsne)
-export(plot_kmer_mismatch)
-export(plot_variability)
 export(pwmDistance)
-export(pwm_distance)
 export(readNarrowpeaks)
-export(read_macs2_narrowpeaks)
 exportMethods("annotationMatches<-")
 exportMethods('counts<-')
 exportMethods(addGCBias)