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

    plotMeta bug when dispersion=NULL & smoothfun!=NULL
    committed Aug 25, 2015
  2. plotMeta bug when dispersion=NULL & smoothfun!=NULL

    plotMeta:
            added !is.null(dispersion) to if closures where I check if dispersion argument is in allowed namespace ("sd","se" or "IQR")
    katwre committed Aug 25, 2015
Commits on Aug 21, 2015
  1. Merge pull request #115 from katwre/master

    improve checking ncol of matrices in heatMeta and plotMeta
    committed Aug 21, 2015
  2. improve checking ncol of matrices in heatMeta and plotMeta

    plotMeata:
     - improve checking number of columns of input matrices
    heatMeta:
     - improve checking number of columns of input matrices
    katwre committed Aug 21, 2015
  3. Merge pull request #114 from katwre/cex_legend_plotTargetAnnotation

    cex.legend to plotTargetAnnotation, faster ScoreMatrixBin, BigWig ext ScoreMatrix(Bin)
    committed Aug 21, 2015
  4. add checking .bigWig, .bigwig extensions in ScoreMatrix(Bin)

    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
    katwre committed Aug 21, 2015
  5. improve example of gffToGranges

    gffToGranges:
       remove split.group arg that doesn't exist anymore in gffToGranges()
    katwre committed Aug 21, 2015
  6. cex.legend arg plotTargetAnnotation;faster ScoreMatrixBin

    plotTargetAnnotation
    - add new argument cex.legend to plotTargetAnnotation() to specify the size of the legend.
    
    ScoreMatrixBin:
      - changed ScoreMatrixBin() to run faster when noCovNA=TRUE
    katwre committed Aug 21, 2015
Commits on Aug 18, 2015
Commits on Aug 14, 2015
  1. Merge pull request #112 from frenkiboy/master

    gffToGRanges update 2
    committed Aug 14, 2015
  2. Description:

    	- 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
    Franke committed Aug 14, 2015
Commits on Aug 13, 2015
  1. readData.R:

    	- changed the removal of " and split.char to make it faster
    Franke committed Aug 13, 2015
  2. Merge pull request #111 from frenkiboy/master

    gffToGRanges update
    committed Aug 13, 2015
  3. DESCRIPTION:

    	- 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
    Franke committed Aug 13, 2015
  4. version bumpo

    Franke committed Aug 13, 2015
  5. readData.R:

    	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
    Franke committed Aug 13, 2015
Commits on Aug 6, 2015
  1. Merge pull request #109 from katwre/master

    plotMeta bug
    committed Aug 6, 2015
Commits on Jul 29, 2015
  1. bug plotMeta dispersion=NULL

    katwre committed Jul 29, 2015
Commits on Jul 22, 2015
  1. Merge pull request #106 from katwre/master

    dispersion, smoothfun, clustfun args changed from by default FALSE to NULL
    committed Jul 22, 2015
Commits on Jul 21, 2015
  1. retrieve deleted line by mistake

    katwre committed Jul 21, 2015
  2. Update NEWS

    committed Jul 21, 2015
  3. Update NEWS

    committed Jul 21, 2015
  4. Update DESCRIPTION

    committed Jul 21, 2015
  5. Update NEWS

    committed Jul 21, 2015
  6. Merge pull request #105 from frenkiboy/master

    ScoreMatrix bug
    committed Jul 21, 2015
Commits on Jul 20, 2015
  1. DESCRIPTION:

    	- version bump
    frenkiboy committed Jul 20, 2015
  2. R/scoreMatrix.R

    	- 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
    frenkiboy committed Jul 20, 2015
Commits on Jul 16, 2015
  1. Merge pull request #104 from katwre/annothub_error

    update DESCRIPTION and NEWS
    committed Jul 16, 2015
  2. update DESCRIPTION

    katwre committed Jul 16, 2015
  3. update NEWS and DESCRIPTION

    katwre committed Jul 16, 2015
  4. Merge pull request #103 from katwre/annothub_error

    improved error in AnnotationHub example
    committed Jul 16, 2015