How to proceed from these methylation .txt files?

Question

[Pin.Bioinf]

Hello, I have been provided many .txt files from a methylation sequencing for different treated and untreated rats. These files have this structure:

for example, file CpG_OB_OT_P5512_1001.txt:

    chr position meth unmeth total degree.of.meth target
chr1 100000912 0 3 3 0 0
chr1 100000960 0 2 2 0 0
chr1 100001014 0 3 3 0 0
chr1 100001022 0 3 3 0 0
chr1 100001073 0 2 2 0 0
chr1 100001199 1 1 2 0.5 0
chr1 100001360 0 1 1 0 0
chr1 100001385 0 3 3 0 0
chr1 100001689 0 2 2 0 0
chr1 100001692 0 2 2 0 0
chr1 100001723 0 1 1 0 0

and also other files that are like this one: CpG_OB_OT_P5512_1002_region_of_interest.txt or target.txt

chr position meth unmeth total degree.of.meth
chr1 1058346 0 1 1 0
chr1 1058391 0 2 2 0
chr1 1058414 0 3 3 0
chr1 1058439 0 2 2 0
chr1 1058461 0 3 3 0
chr1 1058481 1 2 3 0.333
chr1 1058489 0 2 2 0
chr1 1058677 0 2 2 0

I am very very new to this, and I need to do an analysis of correlation between expression values (I already have those) and methylation values. How can I proceed to get the methylation values? are these files to be introduced in R and to be analyzed? Is there any R workflow that uses this kind of structure for methylation analysis? I only have seen people using .idat files. I hope someone can shed some light in this situation. Thank you very much,

Answer 1

[jomo018]

Highlights of a workflow: At this point you have low depth single base methylation figures which are not very informative. You can use R methylKit to create differential regions in the form of BED files. Then, you can correlate these BED files with expression data. You may need to slightly tweak your initial file format to be accepted by methylKit.