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BIMIB-DISCo / TRONCO

Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
https://bimib-disco.github.io/TRONCO
GNU General Public License v3.0
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as.selective.advantage.relations does nothing with caprese models #71

Closed rdiaz02 closed 8 years ago

rdiaz02 commented 8 years ago

As it says: using as.selective.advantage.relations on a caprese model will return NULL, even when we can see there are terms for pr, tp and hg (using, say, as.confidence(themodel, conf = c("pr", "tp", "hg"))).

But the help does not indicate that as.selective.advantage will not work with caprese models.

luca-dex commented 8 years ago

Please, can you paste an example? I'm trying to reproduce the problem without success. What version of TRONCO are you running?

Can you execute the following code? test_dataset_no_hypos is included in TRONCO package

> recon = tronco.caprese(test_dataset_no_hypos)
*** Checking input events.
*** Inferring a progression model with the following settings.
    Dataset size: n = 40, m = 28.
    Algorithm: CAPRESE with shrinkage coefficient: 0.5.
*** Evaluating LogLik informations.
The reconstruction has been successfully completed in 00h:00m:00s 

> as.selective.advantage.relations(recon)
$caprese
                               SELECTS                                SELECTED
1                         ins_del TET2            missense_point_mutations KIT
2                        ins_del ASXL1     missense_point_mutations KRAS_Ex2_3
3                        ins_del ASXL1           missense_point_mutations TET2
4                        ins_del ASXL1           missense_point_mutations EZH2
5      missense_point_mutations SETBP1           nonsense_point_mutations EZH2
6      missense_point_mutations SETBP1          nonsense_point_mutations ASXL1
7  missense_point_mutations NRAS_Ex2_3 missense_point_mutations JARID_2_Ex1_18
8  missense_point_mutations NRAS_Ex2_3          missense_point_mutations IRAK4
9        missense_point_mutations TET2                            ins_del EZH2
10       missense_point_mutations TET2                  nonsense_ins_del CEBPA
11       missense_point_mutations EZH2                            ins_del TET2
12       missense_point_mutations EZH2          missense_point_mutations CEBPA
13       missense_point_mutations EZH2          missense_point_mutations ETNK1
14      missense_point_mutations CSF3R          nonsense_point_mutations CSF3R
15        missense_point_mutations KIT                 nonsense_ins_del RUNX_1
16              nonsense_ins_del CEBPA     missense_point_mutations EED_Ex2_12
17              nonsense_ins_del CEBPA                    nonsense_ins_del WT1
18       nonsense_point_mutations TET2     missense_point_mutations NRAS_Ex2_3
19       nonsense_point_mutations TET2          missense_point_mutations CSF3R
20      nonsense_point_mutations ASXL1     missense_point_mutations CBL_Ex_8_9
21      nonsense_point_mutations ASXL1          missense_point_mutations EPHB3
   OBS.SELECTS OBS.SELECTED TEMPORAL.PRIORITY PROBABILITY.RAISING
1            3            2                 1           0.9302326
2            7            1                 1           0.8510638
3            7            3                 1           0.6961888
4            7            6                 1           0.3578654
5           14            1                 1           0.7407407
6           14            4                 1           0.7407407
7            3            1                 1           0.9302326
8            3            1                 1           0.9302326
9            3            1                 1           0.9302326
10           3            2                 1           0.7945652
11           6            3                 1           0.7352454
12           6            1                 1           0.8695652
13           6            1                 1           0.8695652
14           4            3                 1           0.5874126
15           2            1                 1           0.9523810
16           2            1                 1           0.9523810
17           2            1                 1           0.9523810
18           5            3                 1           0.5050505
19           5            4                 1           0.3666667
20           4            3                 1           0.8169336
21           4            1                 1           0.9090909
   HYPERGEOMETRIC
1    0.0000000000
2    0.0000000000
3    0.0035425101
4    0.0547470547
5    0.0000000000
6    0.0000000000
7    0.0000000000
8    0.0000000000
9    0.0000000000
10   0.0038461538
11   0.0020242915
12   0.0000000000
13   0.0000000000
14   0.0222672065
15   0.0000000000
16   0.0000000000
17   0.0000000000
18   0.0364372470
19   0.0689900427
20   0.0004048583
21   0.0000000000
rdiaz02 commented 8 years ago

I am using the version for BioC devel, downloaded a few days ago. 

> library(help = TRONCO)

        Information on package ‘TRONCO’

Description:

Package:            TRONCO
Version:            2.3.1
Date:               2016-03-23

Yes, your example runs just fine. And I get the same as you. Let me check again why I was not getting the selective advantage.

Actually, I cannot reproduce the error anymore. Sorry for the trouble. I am closing this.