Mercurial > repos > peter-waltman > ucsc_cluster_tools2
comparison cluster.tools/select.k.from.consensus.cluster.R @ 9:a3c03541fe6f draft default tip
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| author | peter-waltman |
|---|---|
| date | Mon, 11 Mar 2013 17:30:48 -0400 |
| parents | a58527c632b7 |
| children |
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| 8:a58527c632b7 | 9:a3c03541fe6f |
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| 195 k.select <- as.numeric( names( k.select ) ) | 195 k.select <- as.numeric( names( k.select ) ) |
| 196 ## find the search range | 196 ## find the search range |
| 197 k.search.range <- (k.select-2):(k.select+2) | 197 k.search.range <- (k.select-2):(k.select+2) |
| 198 k.search.range <- k.search.range[ k.search.range %in% as.numeric( names( vector.of.metric.changes ) ) ] | 198 k.search.range <- k.search.range[ k.search.range %in% as.numeric( names( vector.of.metric.changes ) ) ] |
| 199 k.search.range <- vector.of.metric.changes[ as.character( k.search.range ) ] | 199 k.search.range <- vector.of.metric.changes[ as.character( k.search.range ) ] |
| 200 k.search.range <- k.search.range[ k.search.range < 0.25 ] | 200 |
| 201 k.search.range <- k.search.range[ k.search.range > 0.025 ] | 201 if ( sum( k.search.range < 0.25 ) == 0 ) { |
| 202 ## this should only happen if this is a garbage clustering | |
| 203 k.search.range <- k.search.range[ which.min( k.search.range ) ] | |
| 204 } else { | |
| 205 k.search.range <- k.search.range[ k.search.range < 0.25 ] | |
| 206 } | |
| 207 | |
| 208 if ( sum( k.search.range > 0.025 ) == 0 ) { | |
| 209 k.search.range <- k.search.range[ which.max( k.search.range ) ] | |
| 210 } else { | |
| 211 k.search.range <- k.search.range[ k.search.range > 0.025 ] | |
| 212 } | |
| 202 k.search.range <- names( k.search.range ) | 213 k.search.range <- names( k.search.range ) |
| 203 | |
| 204 | 214 |
| 205 if ( exists("data") ) { | 215 if ( exists("data") ) { |
| 206 ## what direction is the clustering in? rows or cols? | 216 ## what direction is the clustering in? rows or cols? |
| 207 elts <- unique( names( results[[2]]$consensusClass ) ) | 217 elts <- unique( names( results[[2]]$consensusClass ) ) |
| 208 if ( all( elts %in% colnames( data ) ) ) { | 218 if ( all( elts %in% colnames( data ) ) ) { |