SCM

[#6010] The model displayed by ProbABEL is wrong when the interaction_only option is used

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Date:
2015-01-04 21:53
Priority:
3
State:
Closed
Submitted by:
Lennart Karssen (lckarssen)
Assigned to:
Lennart Karssen (lckarssen)
Resolution:
Fixed
Operating System:
All
Severity:
normal
Hardware:
All
Version:
PA v0.4.4
Component:
ProbABEL
URL:
 
Summary:
The model displayed by ProbABEL is wrong when the interaction_only option is used

Detailed description
When using the --interaction_only option (-k) in ProbABEL, the model displayed on the screen is incorrect.

Consider a phenotype file with the following header:
id height cov1 cov2 cov3 cov4 cov5

When running --interaction_only=3, the model that SHOULD be printed is:
Linear model: ( height ) ~ mu + cov1 + cov2 + cov4 + cov5 + SNP_A1 + cov3*SNP_A1
(i.e. without a cov3 term). The model that IS printed is:
Linear model: ( height ) ~ mu + cov1 + cov2 + cov3 + cov4 + cov5 + SNP_A1 + cov3*SNP_A1

This is related to the fix in r1803 (which also seems to have left some debug cout statements in the code).

Followup

Message
Date: 2015-01-04 22:16
Sender: Lennart Karssen

Fixed in r1907 in trunk.
Date: 2015-01-04 22:02
Sender: Lennart Karssen

See bug #5883 (which was apparently not completely fixed in r1803)

Attached Files:

Changes:

Field Old Value Date By
VersionPA trunk2015-01-04 22:16lckarssen
ResolutionAccepted As Bug2015-01-04 22:16lckarssen
close_dateNone2015-01-04 22:16lckarssen
status_idOpen2015-01-04 22:16lckarssen
summaryThe model displayed by ProbABEL is sometimes wrong when the interaction_only option is used2015-01-04 22:06lckarssen
detailsWhen using the --interaction_only option (-k) in ProbABEL, the model displayed on the screen is sometimes incorrect. Consider a phenotype file with the following header: id height cov1 cov2 cov3 cov4 cov5 When running --interaction_only=3, the model that SHOULD be printed is: Linear model: ( height ) ~ mu + cov1 + cov2 + cov4 + cov5 + SNP_A1 + cov3*SNP_A1 (i.e. without a cov3 term). The model that IS printed is: Linear model: ( height ) ~ mu + cov1 + cov2 + cov3 + cov4 + cov5 + SNP_A1 + cov3*SNP_A1 This is related to the fix in r1803 (which also seems to have left some debug cout statements in the code). 2015-01-04 22:04lckarssen
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge