Add methylation analysis methods

[ewafula]

Purpose

Add methylation analysis methods

• Methylation array preprocessing
• Methylation beta-values summaries
• Methylation sample classification

Issue

• Updated methods to include methylation arrays analyses #3

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Method description

Is there anything that you want to discuss further?

PR associated with OpenPedCan-analysis PR # 378 which requires review and merging

Is the pull request ready for review?

Yes

Pull review checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

• All changes to text follow "one sentence per line" [Manubot instructions]
• All citations follow the Manubot citation instructions
• All changes or additions to tables follow the Manubot table instructions
• All figures follow the Manubot figure instructions
• There are no new spelling errors identified by the Manubot spellchecker

Spellcheck Step

The dictionary used for spellchecking can be updated.
Edit the file in build/assets/custom-dictionary.txt by adding new entries to the end.
You do not need to change anything else.
However, if you want to update the first line to have an accurate count of words and you want to remove non-unique ones, run the following command from within build/assets on your favorite OS X or Linux machine:

(( len = $(awk '!a[$0]++' < custom-dictionary.txt | wc -l ) - 1 )); tmpfile="$(mktemp)"; echo "personal_ws-1.1 en $len utf-8" > $tmpfile; tail -n +2 custom-dictionary.txt | awk '!a[$0]++' >> $tmpfile; mv $tmpfile custom-dictionary.txt

[jharenza]

thanks so much @ewafula - made some suggestions and had a question

[jharenza]

approved once the final comment is addressed, thank you!