new data, refseq replaced. scoreMatrix re-written, modCoverage dependency removed
modCoverage.R is removed. and modCoverage class is removed
Changes to inline roxygen comments, starting to work on scoreMatrixBin
first commit for BAM file reading
untested scoreMatrix(BAM,windows) is comitted.
improvements on help section.
modCoverage.R from DESCRIPTION. scoreMatrix is now working with correct options. modRleList is removed from function dispatches.
changes to scoreMatrix() and scoreMatrixBin(). scoreMatrix() should work ok in most cases. scoreMatrixBin() is not in working condition yet.
ordered argument removed for scoreMatrix() function
deleted summarizeModRleList() no need for that with new RleLists
changes to comments. scoreMatrixBin.R has no problems when source().
NAMESPACE issues resolved. package builds and loads with no issues now. no other check is done.
examples added to scoreMatrixBin(). missing "main" argument to image() function in plotMatrix() function
Merge branch 'development' of github.com:al2na/genomation into development
scoreMatrix.R: removed GetViews - it's obsolete
scoreMatrix seems legit now - have to run test though