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License: Freeware

Version: 1.0

Company: University of Hong Kong

Language: English

Size: 10 K

Category: Science & Mathematics

OS support: Windows XP, Windows Server 2003, Windows 2000, Windows Vista, Windows7

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data. To find the p-value from the background, traditional "exact" method needs to sort and search from the whole dataset. It's usage is usually hampered by computing speed, storage and memory limitation when the sample size is too big. FastPval was developed aiming to solve these problems. The main idea of FastPval is to separate the large dataset into smaller parts based on user specified p-value, build model for each part, and calculate the p-values with different model according to the score. Tested on the background from 108 permutations, our method is 0.57 times faster than the conventional method implemented by standard linux sorting and binary search algorithm, and consumes only 1/925 of the memory and 1/901 of storage.

For simplicity, we use two-stage to illustrate this approach on 109 samples. Given a background file, the algorithm first reads through the file and obtains the size of the dataset. It then reads the file again to randomly sample a subset of dataset (105 by default, user specified cutoff N). Since N is sufficiently big, we assume it represents the same distribution as the whole dataset. We then sort the subset and use a cutoff P (0.001 by default, user specified) to obtain a score Sc. Sc will be used to as the cutoff to scan the whole dataset again to select all scores > Sc and put them into second subset. The selection of Sc is very important, it depends on both N and P. N*P should be within the range of 10-1000. If N*P is too small (say 1), the selected Sc does not have enough density in statistics so it is unstable and less reliable. On the other hand, if N*P is too big (say 105), then we put most data into second subset. When the size of the second subset becomes close to the original dataset, the performance improvements become limited.


* Is flexible enough to produce model files and quick to compute P-value;
* Is efficient enough to store two approximate models for reduplicated P-value computation without loading all raw dataset;
* Allow visible GUI interface for the functions of model generating, two stage P-value computation and exact P-value computation using traditional method;
* Is compact enough for model size without loading the whole dataset into memory;

File Distribution Notice of FastPval Freeware -
FastPval Free Download - 2000 Shareware periodically updates software information of FastPval from the publisher, so some information may be slightly out-of-date. You should confirm all information before relying on it. Software piracy is theft, Using FastPval crack, password, registration codes, key generators, serial numbers is illegal.

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