FastQTL specifications
Information
| Unique identifier | OMICS_10934 |
|---|---|
| Name | FastQTL |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS |
| Programming languages | C++ |
| Computer skills | Advanced |
| Version | 2-184 |
| Stability | Stable |
| Maintained | Yes |
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Finding a candidate QTL per phenotype
#1 opened on 2017-10-04 by ale07alvarez • 0 answers
2017-10-04, 05:24
Can someone please explain in detail the meaning of the following section of the paper 2.2 Finding a candidate QTL per phenotype For simplicity, we will focus on a single molecular phenotype P quantified in a set of N samples. Let G be the set of genotype dosages at L variant sites located within a cis-window of 6 W Mb of the genomic location of P. To discover the best candidate QTL for P, FastQTL measures Pearson product-moment correlation coefficients between P and all L variants in G, stores the most strongly correlated variant q [ G as candidate QTL, and assesses its significance by calculating a nominal P-value pn with standard significance tests for Pearson correlation. How can this be affected by a test where only one SNP and its LD proxies (r=0.8) is tested. Thanks!
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