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====OUTPUT FILE FORMATS====
====OUTPUT FILE FORMATS====
=====Summary Statistics=====
* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
* pvalues from the above output are from the family-based single variant score test.
* pvalues from the above output are from the family-based single variant score test.
=====LD Matrices=====
* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
=====Log File=====
* RMW generates a log file with options used:
* RMW generates a log file with options used:
xStart [2699520]
xStart [2699520]
xEnd [154931044]
xEnd [154931044]
=====Graphs=====
* RMW generates QQ plot and Manhattan plots automatically. By using --labelHits option, users can choose whether to label the hits or not. Here is an example:
{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="center" width="100" | [[File:QQ.png]]
|-
| align="center" width="200" | [[File:Single_var_manhattan.png]]
|}
=== Handling Unrelated Individuals ===
=== Handling Unrelated Individuals ===
