Output¶
- pyTEnrich writes two tables per input bed file:
One table for TE subfamily enrichment
One table for TE family enrichment
They both have similar format :
n_i |
n_T.te |
n_T.peak |
expected |
fc.expected |
comparison |
padj.final |
significance |
|
|---|---|---|---|---|---|---|---|---|
SVA_D |
934 |
1433 |
4395 |
2.74 |
250.2 |
peak_in_te |
0 |
**** |
LTR83 |
4 |
724 |
4395 |
0.79 |
2.8 |
te_in_peak |
0.773 |
n.s |
… |
… |
… |
… |
… |
… |
… |
… |
… |
Columns interpretations
First columns represents TE family/subfamily name (Note that this column is not named in output)
- n_i
The overlap found between input bed file and this TE family/subfamily. The size of the overlap rely on Bedtools intersect and the options used for the intersection.
- n_T.te
Total number of loci in the TE subfamily/family.
- n_T.peak
Total number of intervals in input bed files. Typically, the total number of peaks in ChIP-seq.
- expected
Expected overlap between TE group and input bed file, according to a probability derived from TE genome occupancy.
- fc.expected
Fold change between the observed overlap n_i and the expected one expected.
- comparison
Type of comparison that was done for enrichment analysis. Can be either te_in_peak or peak_in_te. For more explanation consult Details methods section.
- padj.final
Adjusted p-value.
- significance
Symbol representing p-value as either
n.s
No significance
*
\(0.01 < p-val \leq 0.05\)
**
\(10^{-3} < p-val \leq 10^{-2}\)
***
\(10^{-4} < p-val \leq 10^{-3}\)
****
\(p-val \leq 10^{-4}\)