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Difference between revisions of "Mgcluster"

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The [[mgcluster]] command ....
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__TOC__
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==Default settings==
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The blast parameter is required...
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  mgcluster(blast=bap.100.blast)
 
  mgcluster(blast=bap.100.blast)
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==Options==
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===name===
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  mgcluster(blast=bap.100.blast, name=bap.100.names)
 
  mgcluster(blast=bap.100.blast, name=bap.100.names)
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===method===
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cluster method: furthest, nearest or average.
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default = furthest
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===cutoff===
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default = 0.70
 
  mgcluster(blast=bap.100.blast, cutoff=1.0)
 
  mgcluster(blast=bap.100.blast, cutoff=1.0)
mgcluster(blast=bap.100.blast, merge=f)
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===precision===
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default = 100
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===merge===
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Default = true, meaning merge after clustering
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mgcluster(blast=bap.100.blast, merge=f)
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===min===
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default = true, meaning use minimum blast score ratio
 
  mgcluster(blast=bap.100.blast, min=f)
 
  mgcluster(blast=bap.100.blast, min=f)
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===length===
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default = 5, minimum overlap
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  mgcluster(blast=bap.100.blast, length=10)
 
  mgcluster(blast=bap.100.blast, length=10)
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===penalty===
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default = 0.10
 
  mgcluster(blast=bap.100.blast, penalty=0.15)
 
  mgcluster(blast=bap.100.blast, penalty=0.15)
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===hcluster===
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default = false, meaning don't use hcluster, use cluster.
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mgcluster(blast=bap.100.blast, hcluster=t)
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[[Category:Commands]]

Revision as of 18:21, 27 January 2010

The mgcluster command ....



Default settings

The blast parameter is required...

mgcluster(blast=bap.100.blast)

Options

name

mgcluster(blast=bap.100.blast, name=bap.100.names)

method

cluster method: furthest, nearest or average. 

default = furthest

cutoff

default = 0.70
mgcluster(blast=bap.100.blast, cutoff=1.0)

precision

default = 100

merge

Default = true, meaning merge after clustering mgcluster(blast=bap.100.blast, merge=f)

min

default = true, meaning use minimum blast score ratio
mgcluster(blast=bap.100.blast, min=f)

length

default = 5, minimum overlap

mgcluster(blast=bap.100.blast, length=10)


penalty

default = 0.10

mgcluster(blast=bap.100.blast, penalty=0.15)

hcluster

default = false, meaning don't use hcluster, use cluster.
mgcluster(blast=bap.100.blast, hcluster=t)