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v1.35.1
Remove code causing error message on some Windows systems; revert v1.33.6 change; minor manual changes
v1.35.0
Bump up version with Bioconductor release
v1.33.6
Try avoid specifying full path to temporary file.
v1.33.5
Add comment to suggest using something other than tempdir() when running code locally
v1.33.4
Change example code to be created in temporary folder instead of current working directory
v1.33.3
Fix typo in comment; change default output to .txt (instead of .xls)
v1.33.2
Add manual 1-variable Rcpp linear regression p-value calculation
v1.33.1
Bump up version and make changes for R-4.0.0 compatibility
v1.29.3
Update DESCRIPTION and README
v1.29.2
Update acknowledgements
v1.29.1
Fix typo in acknowledgement
v1.29.0
Bump up version with newer Bioconductor
v1.27.5
Switch back to earlier description (but still need to bump-up version)
v1.27.4
Bump-up version for hyperlink in description
v1.27.3
Test bumping-up version for minor updates (such as discussion group link) in Bioconductor devel version.
v1.27.2
Add acknowledgements in manual and add authors (and discussion group link).
v1.27.1
Bioconductor version increase to 1.27.0
Then, provide partial update to COHCAP.BSSeq.preprocess() with supplmental annotation script.
Other minor updates.
v1.25.5
Bioconductor-recommended addition of any() function to if-statement in COHCAP.reformatFinalReport()
v1.25.4
Add code in COHCAP.site() to expedite pipeline when p-value is set to 1 (to skip 2-group p-value calculation, if using the Average-by-Site workflow)
v1.25.3
Minor documentation update
v1.25.2
C++ 1-way ANOVA bug fix
v1.25.1
Fix bugs in C++ 2-way ANOVA with constant and/or missing beta values
v1.25.0
Bioconductor bump-up and add experimental c++ code for p-value calculations.
v1.22.3
Set breaks for heatmaps (for either beta values between 0 and 1, or percent methylation between 0 and 100)
v1.22.2
Fix bug for plotting correlations in COHCAP.integrate.avg.by.island() with continuous primary variable.
v1.22.1
Remove QC functions from vignette
v1.22.0
Add COHCAP.reformatFinalReport() function.
v1.21.6
Integrate Average by Island bug fix.
v1.21.5
Average by Island plotting bug fix.
v1.21.4
Fix bug when clustering RRBS data. Change box-plots to have fixed minimum and maximum.
v1.21.3
Allow ANOVA in place of t-test and fix duplicate bug.
v1.21.2
Fixed some bugs with plotting integration results.
v1.21.1
Add random ID to temporary files for COHCAP.integrate.avg.by.island, to avoid potential bug with parallel analysis in same project folder.
v1.19.1
Add clustering option to COHCAP.avg.by.site
v1.19.0
Allow beta quantiles for continuous analysis, instead of maximum / minimum values (although that is still the default)
v1.18.2
Paired 2-group missing value bug fix.
v1.18.1
Continuous pairing bug fix
v1.18.0
Allow use of continuous covariate (switches to linear regression, even if primary variable is categorical)
v1.17.4
Avoid getting heatmap error message
v1.17.3
More debugging for missing values
v1.17.2
Modify upper and lower beta calculations and probe filter for heatmaps
v1.17.1
Add filter for probes with too many missing values in continuous comparison
v1.21.6
Integrate Average by Island bug fix.
v1.21.5
Average by Island plotting bug fix.
v1.21.4
Fix bug when clustering RRBS data. Change box-plots to have fixed minimum and maximum.
v1.21.3
Allow ANOVA in place of t-test and fix duplicate bug.
v1.21.2
Fixed some bugs with plotting integration results.
v1.21.1
Add random ID to temporary files for COHCAP.integrate.avg.by.island, to avoid potential bug with parallel analysis in same project folder.
v1.19.1
Add clustering option to COHCAP.avg.by.site
v1.19.0
Allow beta quantiles for continuous analysis, instead of maximum / minimum values (although that is still the default)
v1.18.2
Paired 2-group missing value bug fix.
v1.18.1
Continuous pairing bug fix
v1.18.0
Allow use of continuous covariate (switches to linear regression, even if primary variable is categorical)
v1.17.4
Avoid getting heatmap error message
v1.17.3
More debugging for missing values
v1.17.2
Modify upper and lower beta calculations and probe filter for heatmaps
v1.17.1
Add filter for probes with too many missing values in continuous comparison
v1.15.2
Fix bug with clusters for continuous variable for COHCAP.avg.by.island()
v1.15.1
Add heatmap to COHCAP.avg.by.island() and COHCAP.site(). Add .csv output to all functions.
v1.15.0
Add de-novo clustering and .csv output for differentially methylated regions options within COHCAP.avg.by.island().
v1.14.5
Allow creation of delta-beta (really max-min beta) .wig files for continuous variable
v1.14.4
Modify continuous variable filter
v1.14.3
Modify COHCAP.avg.by.island() output for continuous variable
v1.14.2
COHCAP.site() bug fix. Add paired continuous analysis. Add code for continuous variable in COHCAP.avg.by.island().
v1.14.1
Minor COHCAP.site() bug fix. Add code for continuous variable.
v1.14.0
Fix COHCAP.avg.by.island() bug. Allow creation of per-sample .wig files
v1.13.8
Allow unmethyl > methyl for COHCAP.avg.by.island() and COHCAP.site()
v1.13.7
Fix COHCAP.integrate.avg.by.site() bug
v1.13.6
Fix COHCAP.avg.by.site() delta beta bug
v1.13.5
Fix possible COHCAP.avg.by.island() bug when outputing boxplots with semi-colons in name
v1.13.4
Fix bug when create.wig is set to FALSE in COHCAP.site(). Add extra troubleshooting statistic to COHCAP.annotate()
Update documentation. Change COHCAP.integrate.avg.by.island() and COHCAP.avg.by.island()output files.
v1.13.3
Added status column to COHCAP.denovo output
v1.13.2
Add COHCAP.denovo function
v1.13.1
Remove empty rows from COHCAP.site()
v1.13.0
Fix COHCAP.annotate() for custom annotation file
v1.12.0
Modify COHCAP.site() so that "Average by Site" workflow can work without replicates
v0.99.4
Update contact information; fix potential bug in ttest2 function
v0.99.5
Switch standard output in warnings() back to print()
v0.99.6
Provide warning() for system() feedback
v0.99.7
Put Perl file paths in quotes; change warning() to message() for system() result
v0.99.8
Remove diagnostics module dependency in Perl scripts.
v0.99.9
Presumably fixed bug (didn't record update in CHANGES file)
v0.99.10
Changed average-by-island message.
v0.99.11
Fixed bug caused when unmethyl.cutoff > methyl.cutoff; changed average-by-island message
v0.99.12
Ignore ambiguous gene annotations; add parameter to focus on only CpG islands mapped to genes
v1.0.0
Automatic bump up with Bioconductor 2.14
v1.0.1
Add "DifferentialMethylation" label in BiocViews
v1.0.2
More descriptive title
v1.1.0
Bump up version
v1.5.0
Bump up version