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

:exclamation: 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)

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 8d19249...3f40959. Read the comment docs.

[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 notifications@github.com 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 (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 .

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[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. notifications@github.com wrote:

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

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[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.