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Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib #126

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jtarraga opened this issue Jun 1, 2017 · 0 comments
Open
6 tasks

Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib #126

jtarraga opened this issue Jun 1, 2017 · 0 comments
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jtarraga commented Jun 1, 2017 •
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The package should provide variant association analysis such as chi-square, linear and logistic regression. Spark's Machine Learning library (MLlib) provides a rich API to implement them in a bigdata environment.

Association tests:

  • Chi-square
  • Logistic regression
  • Linear regression

Taking into account the following genetic models:

  • Dominant
  • Recessive
  • Additive effects of allele dosage
@jtarraga jtarraga self-assigned this Jun 1, 2017
jtarraga added a commit that referenced this issue Jun 1, 2017
@jtarraga
analysis: prepare logistic/linear regression and PCA analysis using S…
39f7008 
…park MLlib, #126
jtarraga added a commit that referenced this issue Jun 1, 2017
@jtarraga
analysis: add analysis files (using Spark MLlib), #126
8e1d038
@jtarraga jtarraga changed the title Implement variant analysis (linear/logistic regression, PCA...) using Spark MLlib Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib Jun 6, 2017
jtarraga added a commit that referenced this issue Jun 7, 2017
@jtarraga
app: implement variant association test CLI, #126
8a0505c
jtarraga added a commit that referenced this issue Jun 7, 2017
@jtarraga
app: add dataset parameter to the association commandline, #126
ddb8d39
jtarraga added a commit that referenced this issue Jun 7, 2017
@jtarraga
test: add junit tests for variant association analysis, #126
3e176bb
jtarraga added a commit that referenced this issue Jun 7, 2017
@jtarraga
appl: tests for accessing nested wrappedarray, #126
a54373c
jtarraga added a commit that referenced this issue Jun 7, 2017
@jtarraga
app: improve variant analysis association (linear and logistic regres…
01f7ead 
…sions), #126
jtarraga added a commit that referenced this issue Jun 9, 2017
@jtarraga
analysis: compute OR from logistic regression coefficient, #126
3e6393d
jtarraga added a commit that referenced this issue Jun 9, 2017
@jtarraga
cli: implements variant plink cli, #126
aab70ef
jtarraga added a commit that referenced this issue Jun 13, 2017
@jtarraga
analysis: improve PLINK analysis (variant command line), #126
d633e7c
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