Obtain the information for specified
node from the output list of ipcaps.
get.node.info(cluster.obj, node)
| cluster.obj | A list returned from the |
|---|---|
| node | An integer representing a node number to enquire information as shown in the HTML output files. |
The return value is NULL if node's information does not exist or a list containing
PCs, eigen.fit, index, and label as explained
below:
$PCs is a matrix of pricipal components of this node.
$eigen.fit is a number represeting the EigenFit value of this
node.
$index is a vector of row number (individuals) of raw.data (input data).
$label is the vector of labels of all individuals that belongs
to this node.
# Importantly, bed file, bim file, and fam file are required # Use the example files embedded in the package BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS") LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS") my.cluster <- ipcaps(bed=BED.file,label.file=LABEL.file,lab.col=2,out=tempdir())#> Running ... IPCAPS #> output: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk #> label file: /private/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T/RtmpYTlCbr/temp_libpath1351142c69ef5/IPCAPS/extdata/ipcaps_example_individuals.txt.gz #> label column: 2 #> threshold: 0.18 #> minimum Fst: 8e-04 #> maximum thread: 1 #> method: mix #> bed: /private/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T/RtmpYTlCbr/temp_libpath1351142c69ef5/IPCAPS/extdata/ipcaps_example.bed #> minimum in group: 20 #> data type: snp #> missing: NA #> In preprocessing step #> Note: the directory '/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk' is existed. #> The result files will be saved to this directory: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1 #> Input data: 103 individuals, 2000 markers #> Start calculating #> Node 1: Start the process #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node1.RData #> Node 1: Check for splitting #> Node 1: Reducing matrix #> Node 1: EigenFit = 0.652486925995028, Threshold = 0.18, no. significant PCs = 3 #> Node 1: Start clustering #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node1.RData #> Node 1: done for clustering #> Time difference of 0.08787107 secs #> Node 1: Checking Fst of group 1 and group 2 #> Node 1: Checking Fst of group 1 and group 3 #> Node 1: Checking Fst of group 1 and group 4 #> Node 1: Checking Fst of group 2 and group 3 #> Node 1: Checking Fst of group 2 and group 4 #> Node 1: Checking Fst of group 3 and group 4 #> Node 1 times took 0.302589178085327 secs #> Node 1: 103 individuals were splitted into: 4 groups #> Node 1: Return status 0 #> Node 1: Split to sub-nodes #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node2.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node3.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node4.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node5.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 1: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 1: Done! #> Time difference of 0.4405329 secs #> Node 2: Start the process #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node2.RData #> Node 2: Check for splitting #> Node 2: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 2: Return status 1 #> Node 2: No split was performed, Status=1 #> Node 2: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/leafnode.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 2: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 2: Done! #> Time difference of 0.03946209 secs #> Node 3: Start the process #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node3.RData #> Node 3: Check for splitting #> Node 3: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 3: Return status 1 #> Node 3: No split was performed, Status=1 #> Node 3: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/leafnode.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 3: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 3: Done! #> Time difference of 0.03794312 secs #> Node 4: Start the process #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node4.RData #> Node 4: Check for splitting #> Node 4: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 4: Return status 1 #> Node 4: No split was performed, Status=1 #> Node 4: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/leafnode.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 4: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 4: Done! #> Time difference of 0.03831792 secs #> Node 5: Start the process #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node5.RData #> Node 5: Check for splitting #> Node 5: Reducing matrix #> Node 5: EigenFit = 0.343228072167861, Threshold = 0.18, no. significant PCs = 3 #> Node 5: Start clustering #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node5.RData #> Node 5: done for clustering #> Time difference of 0.231518 secs #> Node 5: Checking Fst of group 1 and group 2 #> Node 5 times took 0.27881908416748 secs #> Node 5: 100 individuals were splitted into: 2 groups #> Node 5: Return status 0 #> Node 5: Split to sub-nodes #> Node 5: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node6.RData #> Node 5: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node7.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 5: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 5: Done! #> Time difference of 0.440134 secs #> Node 6: Start the process #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node6.RData #> Node 6: Check for splitting #> Node 6: Reducing matrix #> Node 6: EigenFit = 0.0367738545252401, Threshold = 0.18, no. significant PCs = #> Node 6: No split was performed because EigenFit is lower than threshold #> Node 6: Return status 1 #> Node 6: No split was performed, Status=1 #> Node 6: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/leafnode.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 6: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 6: Done! #> Time difference of 0.1011331 secs #> Node 7: Start the process #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/condition.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/rawdata.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/node7.RData #> Node 7: Check for splitting #> Node 7: Reducing matrix #> Node 7: EigenFit = 0.0221170820186458, Threshold = 0.18, no. significant PCs = #> Node 7: No split was performed because EigenFit is lower than threshold #> Node 7: Return status 1 #> Node 7: No split was performed, Status=1 #> Node 7: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/leafnode.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 7: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/RData/tree.RData #> Node 7: Done! #> Time difference of 0.1264801 secs #> In post process step #> Exporting node 2 as group 1 #> Exporting node 3 as group 2 #> Exporting node 4 as group 3 #> Exporting node 6 as group 4 #> Exporting node 7 as group 5 #> Note: save as /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1/groups.txt#> The result files were saved at: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output1 #> Total runtime is 2.40937399864197 sec#Here, to obtain the information of specified node, for example, node 3 node.info <- get.node.info(my.cluster,3) ls(node.info)#> [1] "eigen.fit" "index" "label" "PCs"