HET command usage

[Alexis W]

Hi,

I do not fully understand how the heterogen command should be called. If I have several conditions with several replicates:

Condition_A: A1, A2, A3
Condition_B: B1, B2, B3
Condition_C: C1, C2, C3

For deltapsi my understanding is that I have to run a command for each pair of conditions:

majiq deltapsi \
        -grp1 A1.majiq,A2.majiq,A3.majiq \
        -grp2 B1.majiq,B2.majiq,B3.majiq \
        --names A B
majiq deltapsi \
        -grp1 A1.majiq,A2.majiq,A3.majiq \
        -grp2 C1.majiq,C2.majiq,C3.majiq \
        --names A C
majiq deltapsi \
        -grp1 B1.majiq,B2.majiq,B3.majiq \
        -grp2 C1.majiq,C2.majiq,C3.majiq \
        --names B C

But for heterogen, the groups should be "aggregated as replicates if deltapsi, independently if heterogen", so my understanding is one separate command for each pair of replicates:

majiq heterogen  -grp1 A1.majiq  -grp2 B1.majiq  --names A B
majiq heterogen  -grp1 A1.majiq  -grp2 B2.majiq  --names A B
majiq heterogen  -grp1 A2.majiq  -grp2 B1.majiq  --names A B
majiq heterogen  -grp1 A1.majiq  -grp2 C1.majiq  --names A C
...

Doing this while avoiding to test replicates from the same condition, so not running this:
majiq heterogen  -grp1 A1.majiq  -grp2 A2.majiq  --names A A

Is this understanding correct? Is there example code available somewhere that I missed?

Thank you for your work on this wonderful tool!

[Paul Jewell]

Hello,

Running the samples pair/permutation wise is correct, however, the group names should also be independent / unique for each quantified run.

See this example: https://biociphers.bitbucket.io/majiq-docs-academic/gallery/heterogen-vignette.html#Running-the-MAJIQ-quantifiers

Let me know if this helps to clarify.

Thanks!

[Alexis W]

Hello Paul,

This is very helpful, I had missed the existence of this gallery, it really helps.

But I still don't fully understand what you mean with "the group names should also be independent / unique for each quantified run". Based on the gallery example, the formulation for heterogen is exactly the same as my example above for deltapsi, where groups A, B, C, D are  HepG2_NT, HepG2_SRSF4KD, K562_N, K562_SRSF4KD. In that example each group name is used for 3 comparisons, and the samples are not compared pairwise (i.e. it's the groups that are compared pairwise)?

Are you referring to the builder here? That each sample should have its own group in the [experiment] section of the config file, and it's only at the heterogen stage that we aggregate them by condition?

Thank you!