Incorrect mutation data for gCSI_2017

[ChristopherEeles]

While investigating an issue opened by a user on GitHub I have discovered a problem with the gCSI_2017 mutation data. It appears that the matrix contains expression values instead of the normal strings needed for summarizeMolecularProfiles to work:

> molecularProfiles(gCSI_2017, 'mutation')[1:5, 1:5]
         NCI-H358   NCI-H292   NCI-H522   NCI-H650    NCI-H23
ARID1A -0.4137651 -0.4137651 -0.4137651 -0.4137651 -0.4137651
JAK1   -0.2579865 -0.2579865 -0.2579865 -0.2579865 -0.2579865
MSH2   -0.2113687 -0.2113687 -0.2113687 -0.2113687 -0.2113687
MSH6   -0.3179615 -0.3179615 -0.3179615 -0.3179615 -0.3179615
NFE2L2 -0.1223739 -0.1223739 -0.1223739 -0.1223739 -0.1223739

As such the results returned for summarizeMolecularProfiles are nonsensical:

> assay(summarizeMolecularProfiles(gCSI_2017, 'mutation', summary.stat='and'), 1)[1:5, 1:5]
       NCI-H358 NCI-H292 NCI-H522 NCI-H650 NCI-H23
ARID1A "1"      "1"      "1"      "1"      "1"    
JAK1   "1"      "1"      "1"      "1"      "1"    
MSH2   "1"      "1"      "1"      "1"      "1"    
MSH6   "1"      "1"      "1"      "1"      "1"    
NFE2L2 "1"      "1"      "1"      "1"      "1" 

Please see PharmacoGx issue #71 for more information on the users code and the sessionInfo for their R environment.

[anthfm]

Currently working on this. The compareDrugScreens R package used for this data seems to be incorrect (http://research-pub.gene.com/gCSI-cellline-data/).

[ChristopherEeles]

@imanthonny Any updates on this?

[ChristopherEeles]

@anthfm,

Any updates on this? I would like to close the issue in PharmacoGx.

Best,
Chris

[anthfm]

@ChristopherEeles Unfortunately we are still working on this.