Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/KMeans.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
| author | timpalpant |
|---|---|
| date | Wed, 25 Apr 2012 16:53:48 -0400 |
| parents | b1952a90d4bf |
| children |
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| 11:b1952a90d4bf | 12:81d5b81fb3c2 |
|---|---|
| 12 </outputs> | 12 </outputs> |
| 13 <tests> | 13 <tests> |
| 14 </tests> | 14 </tests> |
| 15 | 15 |
| 16 <help> | 16 <help> |
| 17 | |
| 18 .. class:: warningmark | |
| 19 | |
| 20 This tool requires tabular data in matrix2png format (with column AND row headers). For more information about the required format and usage instructions, see the matrix2png_ website. | |
| 21 | |
| 22 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html | |
| 23 | |
| 24 .. class:: infomark | |
| 25 | |
| 26 You can use the "Align values in a matrix" tool to create a matrix, then use this tool to cluster the matrix with k-means. | |
| 27 | |
| 28 .. class:: infomark | |
| 29 | |
| 30 **TIP:** You can use the **min** and **max** columns to cluster a large matrix based on a subset of the columns. For example, you could cluster a 4000x4000 matrix on columns 200-300 by setting min = 200 and max = 300. This will greatly increase the efficiency of distance calculations during the k-means EM, and also allows you to cluster based on specific regions, such as promoters or coding sequences. | |
| 31 | |
| 32 ----- | |
| 33 | |
| 34 This tool will cluster the rows in an aligned matrix with KMeans_. The implementation builds upon the KMeansPlusPlusClusterer available in commons-math3_. | |
| 35 | |
| 36 .. _KMeans: http://en.wikipedia.org/wiki/K-means_clustering | |
| 37 | |
| 38 .. _commons-math3: http://commons.apache.org/math/ | |
| 39 | |
| 17 </help> | 40 </help> |
| 18 </tool> | 41 </tool> |