tcgaPipeline

[ttriche]

I got tired of writing the same old crap when what I really wanted was to scan an entire directory of IDATs into a GenomicRatioSet with CN values. So here's the fix. (Edit: changed name to tcgaPipeline.)

grSet <- tcgaPipeline(read.metharray.exp(base="."))
show(grSet)
# class: GenomicRatioSet 
# dim: 866836 1 
# metadata(1): SNPs
# assays(2): Beta CN
# ...

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@8d19249). Click here to learn what that means.
The diff coverage is 82.22%.

@@           Coverage Diff            @@
##             master     #96   +/-   ##
========================================
  Coverage          ?   38.3%           
========================================
  Files             ?      32           
  Lines             ?    3428           
  Branches          ?       0           
========================================
  Hits              ?    1313           
  Misses            ?    2115           
  Partials          ?       0

Impacted Files	Coverage Δ
R/rgset.R	55.35% <100%> (ø)
R/tcgaPipeline.R	100% <100%> (ø)
R/generics.R	83.33% <100%> (ø)
R/grset.R	50% <52.94%> (ø)

---

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[ttriche]

I guess I should be adding more unit tests to minfi's base...

…

--t

On Tue, Apr 11, 2017 at 5:06 PM, Codecov ***@***.***> wrote: Codecov <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=h1> Report Merging #96 <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=desc> into master <https://codecov.io/gh/kasperdanielhansen/minfi/commit/ccb6bb05d7206dddbd09017fb58eb026ce593feb?src=pr&el=desc> will *decrease* coverage by 0.24%. The diff coverage is 0%. [image: Impacted file tree graph] <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=tree> @@ Coverage Diff @@## master #96 +/- ## ==========================================- Coverage 36.79% 36.54% -0.25% ========================================== Files 31 31 Lines 3397 3420 +23 ========================================== Hits 1250 1250 - Misses 2147 2170 +23 Impacted Files <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=tree> Coverage Δ R/grset.R <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=tree#diff-Ui9ncnNldC5S> 33.87% <0%> (-12.8%) ⬇️ R/preprocessNoob.R <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=tree#diff-Ui9wcmVwcm9jZXNzTm9vYi5S> 85.88% <0%> (-2.72%) ⬇️ R/generics.R <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=tree#diff-Ui9nZW5lcmljcy5S> 75% <0%> (-6.82%) ⬇️ ------------------------------ Continue to review full report at Codecov <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=continue> . *Legend* - Click here to learn more <https://docs.codecov.io/docs/codecov-delta> Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=footer>. Last update ccb6bb0...b2b9f75 <https://codecov.io/gh/kasperdanielhansen/minfi/pull/96?src=pr&el=lastupdated>. Read the comment docs <https://docs.codecov.io/docs/pull-request-comments> . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#96 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAARIv0olvxz7rBgtws2nW7AxmggdoiJks5rvBWSgaJpZM4MJKVO> .

[ttriche]

Alright I think this is all set. Please merge.

[ttriche]

addendum: check it out, now my pull INCREASES overall unit test coverage. How about that!

[ttriche]

update: noobPipeline() is now tcgaPipeline(), and getSnpBeta() is now a generic. Documentation and tests updated to reflect these changes. This is the enemy of the perfect.

[kasperdanielhansen]

I saw that and I liked it.

…

On Thu, Apr 20, 2017 at 3:58 PM, Tim Triche, Jr. ***@***.***> wrote: addendum: check it out, now my pull INCREASES overall unit test coverage. How about that! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#96 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEuhn1kcbZD6S4T1rlytWr3nosjCD9Zdks5rx7jvgaJpZM4MJKVO> .

[ttriche]

Updated DESCRIPTION to remove conflict. Unclear how this could affect Travis coverage...

[ttriche]

nb. The Travis error is a timeout from taking too long to load the annotation libraries required to run mapToGenome() in the test. Not much I can do about this without dropping the unit test.