7th Column of ALLC file of methyl DMRfind output

[ayfchang]

Hi Yu Peng,

I consistently get 1 on the 7th column of Sample1Sample2.tsv
after methylpy DMRfind

Here is one of the output

9 123461980 - CGC 2 7 1
9 123461988 - CGC 2 7 1
9 123461997 - CGC 1 7 1
9 123462000 - CGT 2 7 1
9 123462003 - CGA 2 7 1
9 123462018 - CGA 3 5 1

In your tutorial, you listed the contents of 7th column as

7 | methylated | 1 | indicator of significant methylation (1 if no test is performed)

I am confused by the statement (1 if no test is performed); what test do you mean here, wheras 1 is input as indicator of significant methylation.

I have found 4 types of output files in the output directory of methylpy DMRfind
Sample1Sample2.tsv
Sample1Sample2_rms_results_collapsed.tsv
Sample1Sample2_rms_results_collapsed_with_levels
Sample1Sample2_rms_results.tsv

whereas rms_results_collapsed.tsv will generate the header below:
#chr start end number_of_dms hypermethylated_samples hypomethylated_sample

And rms_results_collapsed_with_levels will generate the header below:
#chr start end number_of_dms hypermethylated_samples hypomethylated_samples Sample1 Sample2

Finally, rms_results.tsv will generate the header

I have split the header in tab-limited into key terms

0 chr
1 pos
2 strand
3 mc_class
4 pvalue
5 mc_pr1.5k.GSM6574626_allc_CEMBA190423-10A-1-CEMBA190423-10A-2-A1_ad002
6 mc_pr1.5k.GSM6574628_allc_CEMBA190423-10A-3-CEMBA190423-10A-4-C4_ad012
7 h_pr1.5k.GSM6574626_allc_CEMBA190423-10A-1-CEMBA190423-10A-2-A1_ad002
8 h_pr1.5k.GSM6574628_allc_CEMBA190423-10A-3-CEMBA190423-10A-4-C4_ad012
9 frac_pr1.5k.GSM6574626_allc_CEMBA190423-10A-1-CEMBA190423-10A-2-A1_ad002
10 frac_pr1.5k.GSM6574628_allc_CEMBA190423-10A-3-CEMBA190423-10A-4-C4_ad012
11 mc_residual_pr1.5k.GSM6574626_allc_CEMBA190423-10A-1-CEMBA190423-10A-2-A1_ad002
12 mc_residual_pr1.5k.GSM6574628_allc_CEMBA190423-10A-3-CEMBA190423-10A-4-C4_ad012
13 uc_residual_pr1.5k.GSM6574626_allc_CEMBA190423-10A-1-CEMBA190423-10A-2-A1_ad002
14 uc_residual_pr1.5k.GSM6574628_allc_CEMBA190423-10A-3-CEMBA190423-10A-4-C4_ad012
15 num_simulations_sig
16 num_simulations_run

with the corresponding values below

0 15
1 75086731
2 +
3 CGG
4 0.3922
5 7
6 10
7 7
8 11
9 1.0000
10 0.9091
11 0.8209
12 -0.8209
13 -0.8209
14 0.8209
15 100
16 255

As I am new to your software, I hope you can enlighten me on these questions.

Thank you for your attention.

Andrew