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Branch: master
Commits on Aug 25, 2015
  1. Merge pull request #117 from katwre/master

    authored
    plotMeta bug when dispersion=NULL & smoothfun!=NULL
  2. @katwre

    plotMeta bug when dispersion=NULL & smoothfun!=NULL

    katwre authored
    plotMeta:
            added !is.null(dispersion) to if closures where I check if dispersion argument is in allowed namespace ("sd","se" or "IQR")
Commits on Aug 21, 2015
  1. Merge pull request #115 from katwre/master

    authored
    improve checking ncol of matrices in heatMeta and plotMeta
  2. @katwre

    improve checking ncol of matrices in heatMeta and plotMeta

    katwre authored
    plotMeata:
     - improve checking number of columns of input matrices
    heatMeta:
     - improve checking number of columns of input matrices
  3. Merge pull request #114 from katwre/cex_legend_plotTargetAnnotation

    authored
    cex.legend to plotTargetAnnotation, faster ScoreMatrixBin, BigWig ext ScoreMatrix(Bin)
  4. @katwre

    add checking .bigWig, .bigwig extensions in ScoreMatrix(Bin)

    katwre authored
    ScoreMatrixBin:
      - check not only for .bw but also .bigWig and .bigwig extenstions of BigWig file
    
    ScoreMatrix:
      - check not only for .bw but also .bigWig and .bigwig extensions of BigWig file
  5. @katwre

    improve example of gffToGranges

    katwre authored
    gffToGranges:
       remove split.group arg that doesn't exist anymore in gffToGranges()
  6. @katwre

    cex.legend arg plotTargetAnnotation;faster ScoreMatrixBin

    katwre authored
    plotTargetAnnotation
    - add new argument cex.legend to plotTargetAnnotation() to specify the size of the legend.
    
    ScoreMatrixBin:
      - changed ScoreMatrixBin() to run faster when noCovNA=TRUE
Commits on Aug 18, 2015
  1. @katwre
Commits on Aug 14, 2015
  1. Merge pull request #112 from frenkiboy/master

    authored
    gffToGRanges update 2
  2. Description:

    Franke authored
    	- added GenomeInfoDb in Imports (contains the "seqlevels" generic)
    
    Namespace:
    	- imported seqlevels from GenomeInfoDb
    
    News:
    	- added the changes to gffToGRanges
    
    readData.R:
    	- changed the gffToGRanges to be a wrapper to import from rtracklayer
    
    test_readData.R:
    	- tests for gffToGRanges
Commits on Aug 13, 2015
  1. readData.R:

    Franke authored
    	- changed the removal of " and split.char to make it faster
  2. @katwre
  3. Merge pull request #111 from frenkiboy/master

    authored
    gffToGRanges update
  4. DESCRIPTION:

    Franke authored
    	- reordered Suggest and Depends to be alphabetically sorted
    
    readData.R:
    	- added data.table:: to functions from the data.table package
    
    test_readData.R
    	- added functions for testing gffToGRanges
  5. version bumpo

    Franke authored
  6. readData.R:

    Franke authored
    	gffToGRanges
    		- corrected bug which caused the function to break when column 9 didn't have
    		equal number of elements in each row. Now implemented using data table
    		- added ensembl argument, prepends chr to gff files from ENSEMBL
    		- documentation made a bit more verbose
    
    test.gtf:
    	- gtf file used for testing
Commits on Aug 6, 2015
  1. Merge pull request #109 from katwre/master

    authored
    plotMeta bug
Commits on Jul 29, 2015
  1. @katwre
  2. @katwre

    bug plotMeta dispersion=NULL

    katwre authored
Commits on Jul 22, 2015
  1. Merge pull request #106 from katwre/master

    authored
    dispersion, smoothfun, clustfun args changed from by default FALSE to NULL
  2. @katwre
Commits on Jul 21, 2015
  1. @katwre
  2. @katwre
  3. Update NEWS

    authored
  4. Update NEWS

    authored
  5. Update DESCRIPTION

    authored
  6. Update NEWS

    authored
  7. Merge pull request #105 from frenkiboy/master

    authored
    ScoreMatrix bug
Commits on Jul 20, 2015
  1. @frenkiboy

    DESCRIPTION:

    frenkiboy authored
    	- version bump
  2. @frenkiboy

    R/scoreMatrix.R

    frenkiboy authored
    	- fixed a bug in scoreMatrix which happened when the target Rle
    	  was not sorted by ASCI - there was a chromosome mismatch
    
    *.Rd
    	- documentation files were updated
Commits on Jul 16, 2015
  1. Merge pull request #104 from katwre/annothub_error

    authored
    update DESCRIPTION and NEWS
  2. @katwre

    update DESCRIPTION

    katwre authored
  3. @katwre

    update NEWS and DESCRIPTION

    katwre authored
  4. Merge pull request #103 from katwre/annothub_error

    authored
    improved error in AnnotationHub example
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