CRAN
aSPU 1.48
Adaptive Sum of Powered Score Test
Released Jun 24, 2017 by Il-Youp Kwak
Dependencies
fields 9.6 MASS 7.3-50 gee 4.13-19 mvtnorm 1.0-8 matrixStats 0.53.1
R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single nucleotide polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended 'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Installation
Maven
This package can be included as a dependency from a Java or Scala project by including
the following your project's pom.xml
file.
Read more
about embedding Renjin in JVM-based projects.
<dependencies> <dependency> <groupId>org.renjin.cran</groupId> <artifactId>aSPU</artifactId> <version>1.48-b13</version> </dependency> </dependencies> <repositories> <repository> <id>bedatadriven</id> <name>bedatadriven public repo</name> <url>https://nexus.bedatadriven.com/content/groups/public/</url> </repository> </repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:aSPU')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.
- GATES2-examples
- GEEaSPU-examples
- GatesSimes-examples
- Hyst-examples
- MTaSPUs-examples
- MTaSPUsSet-examples
- MTaSPUsSetPath-examples
- MTaSPUsSetScore-examples
- SAMD11-examples
- aSPU-examples
- aSPUd-examples
- aSPUpath-examples
- aSPUpath2-examples
- aSPUr-examples
- aSPUs-examples
- aSPUsD-examples
- aSPUsPath-examples
- aSPUsPath2-examples
- aSPUw-examples
- estcov-examples
- exdat-examples
- getlogitp-examples
- kegg9-examples
- minP-examples
- plotPmat-examples
- pruneSNP-examples
- simPathAR1Snp-examples
- someGs-examples