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The weights provided to the smoothing function should be the inverse standard deviation of the methylation difference coefficient, since we want to place more weight on observations with less variation.
…/GENCODE This commit resolves #15 by adding the arguments `mappingInfo` and `simplifyGeneID` to `annotateTranscripts()`. `mappingInfo` is a named list whose elements are passed to `AnnotateDbi::mapIds()` for more flexible gene id matching between a given TxDb object and the organism package (like org.Hs.eg.db). `simplifyGeneId` is a logical and if TRUE gene ids like `ENSTsomething.8_etc` get simplified to `ENSTsomething`. This allows working with TxDb objects created from GENCODE GTF files and matching then to org.Hs.eg.db as if the ids were ENSEMBL gene ids. A unit test checking the new changes has been added as well. A check and build reveals no new notes/warnings/errors. ``` $ R CMD build --keep-empty-dirs --no-resave-data bumphunter Loading required package: colorout * checking for file ‘bumphunter/DESCRIPTION’ ... OK * preparing ‘bumphunter’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘bumphunter_1.17.2.tar.gz’ $ R CMD check --no-vignettes --timings bumphunter_1.17.2.tar.gz Loading required package: colorout * using log directory ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck’ * using R version 3.4.0 (2017-04-21) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bumphunter/DESCRIPTION’ ... OK * this is package ‘bumphunter’ version ‘1.17.2’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘foreach’ ‘iterators’ ‘parallel’ ‘locfit’ Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘bumphunter’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘doParallel:::.options’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bumphunterEngine: no visible binding for global variable ‘bootstraps’ Undefined global functions or variables: bootstraps * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck/00check.log’ for details. ```
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@71633 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@71742 bc3139a8-67e5-0310-9ffc-ced21a209358
Various file additions and deletions. git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@71939 bc3139a8-67e5-0310-9ffc-ced21a209358
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… of -area git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@72097 bc3139a8-67e5-0310-9ffc-ced21a209358
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@72694 bc3139a8-67e5-0310-9ffc-ced21a209358
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…earest git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@73216 bc3139a8-67e5-0310-9ffc-ced21a209358
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…lects TRUE semantic, old name will be deprecated soon) git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@113044 bc3139a8-67e5-0310-9ffc-ced21a209358
build cycle) was DECREMENTED back to 1.9.z. Version numbers cannot be decremented as there is no way for users to install the resulting package (R will always install the most recent version). Bumping the version to 1.11.2. Do NOT decrement it again, please. git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@113121 bc3139a8-67e5-0310-9ffc-ced21a209358
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From: Martin Aryee <martin.aryee@gmail.com> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@115313 bc3139a8-67e5-0310-9ffc-ced21a209358
From: lcolladotor <lcollado@jhsph.edu> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@115319 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
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From: Samuela Pollack <sampoll@users.noreply.github.com> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@129747 bc3139a8-67e5-0310-9ffc-ced21a209358
…/GENCODE This commit resolves #15 by adding the arguments `mappingInfo` and `simplifyGeneID` to `annotateTranscripts()`. `mappingInfo` is a named list whose elements are passed to `AnnotateDbi::mapIds()` for more flexible gene id matching between a given TxDb object and the organism package (like org.Hs.eg.db). `simplifyGeneId` is a logical and if TRUE gene ids like `ENSTsomething.8_etc` get simplified to `ENSTsomething`. This allows working with TxDb objects created from GENCODE GTF files and matching then to org.Hs.eg.db as if the ids were ENSEMBL gene ids. A unit test checking the new changes has been added as well. A check and build reveals no new notes/warnings/errors. ``` $ R CMD build --keep-empty-dirs --no-resave-data bumphunter Loading required package: colorout * checking for file ‘bumphunter/DESCRIPTION’ ... OK * preparing ‘bumphunter’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘bumphunter_1.17.2.tar.gz’ $ R CMD check --no-vignettes --timings bumphunter_1.17.2.tar.gz Loading required package: colorout * using log directory ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck’ * using R version 3.4.0 (2017-04-21) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bumphunter/DESCRIPTION’ ... OK * this is package ‘bumphunter’ version ‘1.17.2’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘foreach’ ‘iterators’ ‘parallel’ ‘locfit’ Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘bumphunter’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘doParallel:::.options’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bumphunterEngine: no visible binding for global variable ‘bootstraps’ Undefined global functions or variables: bootstraps * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck/00check.log’ for details. ``` From: Leonardo Collado Torres <lcollado@jhsph.edu> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@129748 bc3139a8-67e5-0310-9ffc-ced21a209358
From: sampoll <sampoll@users.noreply.github.com> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter@129749 bc3139a8-67e5-0310-9ffc-ced21a209358
The version number has been updated after cherry picking commit ac34111.
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