How to test for overlap between two gene lists?
MlFinLab helps traders build strategies, based on the latest academic research. Given two gene lists, tests the significance of their overlap in comparison with a genomic background. The null hypothesis is that the odds ratio is no larger than 1.
How to find the intersection of two genomic ranges?
In cases of multiple overlaps, one could use intersect (), then findOverlaps () with that and then continue on with the procedure demonstrated above (or iterate over the overlaps). Thanks for contributing an answer to Bioinformatics Stack Exchange!
Which is more memory efficient intersect or findoverlaps?
It’d be more memory efficient to iterate over o, but this gives you the idea. In cases of multiple overlaps, one could use intersect (), then findOverlaps () with that and then continue on with the procedure demonstrated above (or iterate over the overlaps).
How to calculate the significance of an overlap?
Calculate the significance of the overlap of two groups of genes drawn from the set of genes in the genome. Number of genes in set 1. Number of genes in set 2. Overlap between set 1 and set 2. Number of genes in the genome. (For the Kim lab full genome microarray, 17611 is the number of good spots.)
Which is the null hypothesis for two gene lists?
Given two gene lists, tests the significance of their overlap in comparison with a genomic background. The null hypothesis is that the odds ratio is no larger than 1. The alternative is that the odds ratio is larger than 1.0. It returns the p-value, estimated odds ratio and intersection.
Which is faster Fisher’s exact test or dhyper?
The Jaccard index is a measurement of similarity between two sets. It is defined as the number of intersections over the number of unions. Although Fisher’s exact test is chosen for implementation, it should be noted that the R implementation of Fisher’s exact test is slower than using dhyper directly.