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Minor documentation fixes.

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commit f3762e4b919429e849066ced0409e323f0435d80 1 parent 7935fbd
Francesco Napolitano authored
Showing with 5 additions and 167 deletions.
  1. +3 −2 INSTALL.txt
  2. +2 −0  build/README.txt
  3. +0 −165 samples/test.lf
5 INSTALL.txt
View
@@ -14,7 +14,8 @@ Then to build lglc:
> make
-Or to install it:
+Or to install it (make sure you have proper permissions - aka root -
+to do this):
> make install
@@ -27,5 +28,5 @@ You should get a file named test.lf.dot. If you have Graphviz
installed (http://www.graphviz.org), you can obtain a pdf graph
visualization this way:
- > dot test.lf.dot -o test.pdf
+ > dot -Tpdf test.lf.dot -o test.pdf
2  build/README.txt
View
@@ -0,0 +1,2 @@
+This is an empy build directory, meant to be used as cmake output. Run
+"cmake .." from here.
165 samples/test.lf
View
@@ -6,168 +6,3 @@
@4<
\5->@1,@10
;
-
-/*
-LogR_BAF_FileName[F] -> prepareInput[F];
-
- /getSampleNames
- | -> CNVboolVects,
- | exportDistMats [F],
- | intersMat_genes,
- | exportIntersMat_genes [F],
- | exportCNVDiffMat [F],
- | clustergram [F],
- | distMatGfx [F],
- | CNVDiffMat,
- | countCNVlenghts,
- | exportToCircos,
- | intersectRegs,
- | intersectTBRegs
- sampleSheet[F] <
- \ /genoTypeCheck
- @prepareInput <
- \ /makeBed [F]
- PennCNV[F] |
- -> joinPennCNVout[F] <
- \
- | /exportPerRegion [F]
- | | -> @exportToCircos
- | reformat2 <
- | / \ @countCNVlenghts
- | | | -> exportCNVlenghts [F],
- | | | exportFigCNVlenghts [F]
- addGeneInfo[F] |
- -> readFile <
- \
- | /getGeneNames
- | | -> @intersMat_genes,
- | | @clustergram,
- | | @exportIntersMat_genes,
- | | @CNVDiffMat,
- | | @exportCNVDiffMat
- manualClean <
- \ /@intersectRegs
- | | ->
- | | exportMergedRegs [F]
- .<
- \
- | /exportMergedRegsTB [F]
- | @intersectTBRegs<
- | / \mergeFragments
- | | | -> exportMergedFragments [F],
- | | | exportFigExtRegs [F]
- .<
- \
- | /exportPerRegion_clean [F]
- | .<
- | / \CompareRegionAndGenes
- | | -> exportComRegGen [F]
- reformat <
- \ /@intersMat_genes
- | | -> @exportIntersMat_genes
- addStats <
- \ /@exportCNVDiffMat,
- | | @clustergram
- | @CNVDiffMat <
- | / \ computeFisher
- | | | -> @clustergram,
- | | | @exportCNVDiffMat
- .<
- \ /@exportCNVDiffMat
- .<
- \
- | /@intersMat_genes
- | | -> @exportIntersMat_genes
- @CNVboolVects <
- \ samplesDistMats
- | -> @exportDistMats,
- | @distMatGfx
-;
-*/
-
-/*
-
- /MDS
- .<
- / \Boxplot
- .<
- / \ /HClustering -> PlotHClust
- | .<
- | \Kmeans -> PlotClust
- irisdata -> Normalize <
- \ /@PlotClust
- labels<
- \@PlotHClust
-;
-
-*/
-
-/*
-[color = limegreen] adenine:
- /N ^2^ -> C -> N -> C1
-H,H ^1^ <- N -> C <
- \ /@C1
- C <
- \N -> C -> ^4^ N ->@C1
-;
-
-
-
-[color = mediumpurple] guanine:
- /N -> C2
- C<
- / \C3 -> ^4^ N -> @C2
-O ^6^ ->C<
- \ /H ^7^
- N<
- \ /N -> @C3
- C<
- \N->H,H ^8^
-;
-
-
-
-[color = orchid] thymine:
- /^4^ N1
- C<
- / \O
- N<
- / \^2^ H
-^1^ O->C<
- \ /C
- C<
- \C-> @N1
-;
-
-
-[color = salmon] cytosine:
- /^8^ O
- ^7^ N->C<
- / \^4^ N1
-^6^ H,H <- N ->C<
- \C -> C -> @N1
-;
-
-
-
-[color = gray90] nucleotide:
- /O2
- C1 ^4^ ->C2<
- / \H2
-O<
- \ /O->P->O,^5^O,O^5^
- C4<
- \ /@C2
- C3<
- \O3
-;
-
-
-
-@nucleotide -> @adenine;
-nucleotide -> @cytosine;
-nucleotide -> @thymine;
-nucleotide -> @guanine;
-@adenine -> @thymine;
-@guanine -> @cytosine;
-*/
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