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Revision as of 07:36, 12 March 2010 (view source) Igchoi (Talk | contribs) (→Data) ← Older edit		Revision as of 07:40, 12 March 2010 (view source) Igchoi (Talk | contribs) (→Results) Newer edit →
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	==Results==		==Results==
		+	===MDS===
		+	*Procedures
		+	#build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [ref:euclidean distance]
		+	#do MDS (multidimensional scaling) of the distance matrix
		+	#get coordinates from the first three dimension and plot them in a 3D-space
		+	*Exact distance matrix
		+
	==R script sources==		==R script sources==

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Revision as of 07:40, 12 March 2010

Contents 1 Pan-Genomic Universe 1.1 Data 1.2 Results 1.2.1 MDS 1.3 R script sources

Pan-Genomic Universe

Data

• Pan-Genome data version 0.1 Feb 2010
• Download the frequency profile (1,137 genomes x 11,912 pfam domains)
  • download: The FP(Frequency Profile) matrix

Results

MDS

• Procedures

1. build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [ref:euclidean distance]
2. do MDS (multidimensional scaling) of the distance matrix
3. get coordinates from the first three dimension and plot them in a 3D-space

• Exact distance matrix

R script sources