TCC Bug fix and Extensions#2

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jsun wants to merge 157 commits intotomoakin:masterfrom

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Commits on Feb 28, 2013

Adjust white space
kohijiri
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Rewrite NEWS and CIATION files in inst directory
kohijiri
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Adjust white space
kohijiri
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Split out .normByXxx methods from main list of TCC methods field
kohijiri
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Add row.names automatically if the data doesnt have row name at TCC constructor
kohijiri
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The elements of DEGES.potentialDEG only use '1' to indicate DEG. Fixed to use '1' or '2' for indicating DEG.
kohijiri
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Add col.tag for plotting MA plot
kohijiri
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change the order of returned value of plotMA
kohijiri
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round the decimal to integer before analysis
kohijiri
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changed version to v1.0.1
kohijiri
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reWrite test script
kohijiri
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Commits on Mar 4, 2013

Add 'show' method for TCC class.
kohijiri
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Add 'names' method for TCC class.
kohijiri
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Add more information to show TCC class object. Because the previous one is too simple.
kohijiri
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Commits on Mar 5, 2013

Commits on Mar 7, 2013

Add depending package of 'snow'.
kohijiri
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Attach the 'man' of names, length, [ and show together on the 'man' of TCC-class.
kohijiri
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Attach the 'man' of names, length, [ and show method together on the 'man' of TCC-class.
kohijiri
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removed unnecessary files. and add show, length, names method test script.
kohijiri
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remove unnecessary files with 'git rm' command
kohijiri
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Commits on Mar 8, 2013

Add vignette to TCC package.
kohijiri
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Commits on Mar 19, 2013

Commits on Mar 21, 2013

Change the expression labels of 'show' function.
kohijiri
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Commits on Mar 22, 2013

Commits on Mar 24, 2013

the file which has forgetten to commit. (?)
kohijiri
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add citation (about GLM of edgeR).
kohijiri
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Commits on Mar 25, 2013

Modify the wrong method of p.adjust in DEGES/DESeq(GLM).
kohijiri
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minor change
kohijiri
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Commits on Mar 27, 2013

Re moved 'processors' argument in TCC. The 'cl' argument is used for baySeq.
kohijiri
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modify the test scripts.
kohijiri
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add GLM (multi-group, multi-factor) test scripts.
kohijiri
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change depended packages.
kohijiri
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Commits on Mar 28, 2013

Commits on Mar 29, 2013

Change 'DEG.foldchange' argument.
kohijiri
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i mistake the conditional judgement in 'testByDeseq'
kohijiri
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Some inconvenience was happend when execute vignette code, move the packages from 'imports' to 'depends'.
kohijiri
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Change 'names' field in TCC class to 'gene_id'.
kohijiri
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Commits on Apr 1, 2013

Change 'length' function. Return the count object if it was called.
kohijiri
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Commits on Apr 2, 2013

Commits on Apr 11, 2013

remove gamma model
kohijiri
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Commits on Apr 14, 2013

vignette for TCC package
kohijiri
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Commits on Apr 16, 2013

Rewrite 'subset' and '[' functions
kohijiri
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spell miss
kohijiri
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Commits on Apr 17, 2013

Commits on Apr 21, 2013

Minor changed for adjusting the position of figures. Add pdf file.
kohijiri
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delete geometry.sty in Rnw.
kohijiri
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Commits on Apr 22, 2013

Commits on Apr 23, 2013

change figure format to PNG from EPS of vignette.
kohijiri
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Commits on Apr 26, 2013

Commits on Apr 29, 2013

Remove the code which contains the unsed argument ('processors').
kohijiri
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Commits on May 3, 2013

bug fix
kohijiri
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bug fix
kohijiri
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Commits on May 10, 2013

Add .getRank method code, but unsed.
kohijiri
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Fix Rd files for avoding CMD check warnings.
kohijiri
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Commits on May 11, 2013

Add pre-PDEG value in private field.
kohijiri
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Commits on May 12, 2013

delete debug code
kohijiri
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comment the 'increment' argument function.
kohijiri
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minor change the citations.
kohijiri
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modify the vignette.
kohijiri
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Commits on May 13, 2013

modify the vignette.
kohijiri
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Commits on May 14, 2013

add if sentence for avoding check
kohijiri
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modify the Rd files
kohijiri
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modify TCC vignette
kohijiri
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change the version number
kohijiri
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Commits on May 15, 2013

add package tar
kohijiri
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Commits on May 18, 2013

rename the test script.
kohijiri
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Commits on May 22, 2013

bug fix. the col.tag argument doesnt work correctly.
kohijiri
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Commits on May 23, 2013

modify manuals
kohijiri
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Commits on May 24, 2013

delete package
kohijiri
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Commits on May 29, 2013

bug fix. the col option does not work correctly
kohijiri
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Commits on May 30, 2013

modify manuals
kohijiri
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Commits on Jun 4, 2013

fix bug.
kohijiri
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Commits on Jun 5, 2013

use 4 spaces per indentation level and shorten the lines less than 80 columns
kohijiri
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Commits on Jun 6, 2013

add unit test
kohijiri
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delete test scripts
kohijiri
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Commits on Jun 7, 2013

modify vignette
kohijiri
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change to correctly format
kohijiri
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modify author name
kohijiri
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move NEWS to correctly directory
kohijiri
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Commits on Jun 16, 2013

add twad method
zhuque
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Commits on Jun 17, 2013

add wad test
kohijiri
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bug fix for twad method
kohijiri
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bug fix for .testByWad method
kohijiri
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Commits on Jun 18, 2013

bug fix for twad method
kohijiri
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Commits on Jun 27, 2013

bug fix for TWAD normalization
kohijiri
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add parameters for TWAD nromalization
kohijiri
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add increment argument for caclNormFactors.
kohijiri
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Commits on Jul 9, 2013

Add AD argument for TWAD normalization.
kohijiri
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the submitted article has been published
kohijiri
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Commits on Jul 11, 2013

the article has been published.
kohijiri
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Commits on Jul 14, 2013

add arguments for TWAD method
kohijiri
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Commits on Jul 18, 2013

split file
kohijiri
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Commits on Jul 21, 2013

Commits on Jul 22, 2013

remvoed depended package
kohijiri
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add new test method
kohijiri
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split file
kohijiri
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Commits on Jul 27, 2013

change writting style
kohijiri
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change meta files
kohijiri
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delete AD argument in WAD
kohijiri
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add unit tests
kohijiri
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remove
kohijiri
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delete AD argument in WAD
kohijiri
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change function used in ROKU
kohijiri
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bug fix
kohijiri
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delete AD argument of WAD
kohijiri
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Commits on Jul 30, 2013

adjust arguments
kohijiri
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let function can generate multiple factor simulation data
kohijiri
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Commits on Jul 31, 2013

change meta files
kohijiri
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fix code
kohijiri
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adjust document files
kohijiri
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add microarray data
kohijiri
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Commits on Aug 6, 2013

add ... argument
kohijiri
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Commits on Aug 7, 2013

bug fix and add paried strategy
kohijiri
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man file
kohijiri
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add unittest
kohijiri
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Commits on Aug 8, 2013

simulation data
kohijiri
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Commits on Aug 9, 2013

Commits on Aug 26, 2013

meta file, delete NOISeq
kohijiri
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bug fix
kohijiri
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delete duplicated files
kohijiri
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bug fix test script
kohijiri
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change man files
kohijiri
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Commits on Aug 28, 2013

fix code
kohijiri
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vignette change
kohijiri
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delete paired strategy
kohijiri
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change README
kohijiri
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change README
kohijiri
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fix
kohijiri
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add hypo data
kohijiri
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change data
kohijiri
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Commits on Aug 29, 2013

fix data
kohijiri
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delete space
kohijiri
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Commits on Sep 10, 2013

fix comment in TCC.Rnw
Kohijiri
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change unit test threhold
Kohijiri
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change released url
Kohijiri
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Commits on Sep 30, 2013

delete vignette
Kohijiri
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