This is a fork of the methylPipe Bioconductor package (https://github.com/Bioconductor-mirror/methylPipe). Some of the functions in the original package is not compatible with non-UCSC genomes, as a result it is not most suitable for custom genomes. I have made the following changes to fix this.

1. methstats()

• line 548 - disable dev.new() when using pdf()

1. BSprepare()

• line 187 - add "addchr" switch
• line 226 - check "addchr"

2. plotMeth()

• line 825 - add "ucscOrg" switch and band dataframe required if ucscOrg=FALSE
• line 886-894 - use custom band dataframe to create Ideogram track with custom genome