Single Marker Association 2.0 review
DownloadSingle Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/co
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Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/control dichotomy.
Usage:
The tool reads two files as input, the first is a set of case and the second a case of control haplotypes. The format of the files is one line per haplotype, where the SNP data is represented as 0 or 1, separated by white-space.
The tool outputs a list of statistics for each marker
The marker number (from left to right in the input data)
The frequency of the 0 allele for the cases file
The chi-square contingency table statistics for the marker
The CDF of the chi-square statistics
The p-value of the statistics (1-CDF)
Installation:
The SMA tool is written in C++. It should compile on any Unix like system. To install, download the source code and unpack it (tar xzf sma-v.tar.gz, where v is the version number of sma), then run make in the subdirectory sma-v created during unpacking.
What's New in This Release:
Support for (unphased) genotype data.
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