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ipcaps2's Introduction

IPCAPS2

R-CMD-check CRAN status codecov License: GPL v3 Lifecycle: maturing DOI FOSSA Status

IPCAPS2 is an unsupervised clustering algorithm based on iterative pruning to capture population structure. This version supports ordinal data which can be applied directly to SNP data to identify fine-level population structure and it is built on the iterative pruning Principal Component Analysis (ipPCA) algorithm by Intarapanich et al. (2009) <doi: 10.1186/1471-2105-10-382> and Limpiti et al. (2011)<doi: 10.1186/1471-2105-12-255>. The IPCAPS2 involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and Clustering EM estimation as in Lebret et al. (2015) <doi: 10.18637/jss.v067.i06>. In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package KRIS.

Installation

You can install the released version of IPCAPS2 from CRAN with:

install.packages("IPCAPS2")

Alternatively, you can install the dev version of IPCAPS2 from Github with

install.packages("remotes")
remotes::install_github("kridsadakorn/ipcaps2", dependencies = TRUE)

Document

You can see the reference manual from: https://www.biostatgen.org/ipcaps/

Example

This is a basic example which shows you how to use the packages:

library(IPCAPS2)

BED.file <- system.file("extdata", "ipcaps_example.bed", package = "IPCAPS2")
LABEL.file <- system.file("extdata", "ipcaps_example_individuals.txt.gz",
                          package = "IPCAPS2")
my.cluster1 <- ipcaps2(bed = BED.file, label.file = LABEL.file, lab.col = 2,
out = tempdir())
#> Running ... IPCAPS2 
#>  output: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6 
#>  label file: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/IPCAPS2/extdata/ipcaps_example_individuals.txt.gz
#>  label column: 2
#>  threshold: 0.18
#>  minimum Fst: 8e-04
#>  maximum thread: 1
#>  method: mix
#>  bed: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/IPCAPS2/extdata/ipcaps_example.bed
#>  minimum in group: 20
#>  data type: snp
#>  missing: NA
#> In preprocessing step
#> Note: the directory '/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6' is existed. 
#> The result files will be saved to this directory: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output 
#> Input data: 103 individuals, 2000 markers
#> Start calculating
#> Node 1: Start the process
#> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/node1.RData
#> Node 1: done for clustering
#> Time difference of 0.146003 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 0.364345073699951 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//Rtmp45z1n6/cluster_output/RData/node2.RData
#> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/node3.RData
#> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/node4.RData
#> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/node5.RData
#> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 1: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 1: Done!
#> Time difference of 0.6429439 secs
#> Node 2: Start the process
#> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/leafnode.RData
#> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 2: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 2: Done!
#> Time difference of 0.03293204 secs
#> Node 3: Start the process
#> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/leafnode.RData
#> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 3: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 3: Done!
#> Time difference of 0.0298121 secs
#> Node 4: Start the process
#> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/leafnode.RData
#> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 4: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 4: Done!
#> Time difference of 0.02961802 secs
#> Node 5: Start the process
#> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/node5.RData
#> Node 5: done for clustering
#> Time difference of 0.1203899 secs
#> Node 5: Checking Fst of group 1 and group 2
#> Node 5 times took 0.163332223892212 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//Rtmp45z1n6/cluster_output/RData/node6.RData
#> Node 5: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/node7.RData
#> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 5: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 5: Done!
#> Time difference of 0.3226371 secs
#> Node 6: Start the process
#> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/leafnode.RData
#> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 6: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 6: Done!
#> Time difference of 0.134871 secs
#> Node 7: Start the process
#> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/condition.RData
#> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/rawdata.RData
#> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/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//Rtmp45z1n6/cluster_output/RData/leafnode.RData
#> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 7: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output/RData/tree.RData
#> Node 7: Done!
#> Time difference of 0.114059 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//Rtmp45z1n6/cluster_output/groups.txt
#> The result files were saved at:  /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output 
#> Total runtime is 2.42903804779053 sec

The function ipcaps does unsupervised clusering, and here is the result:

table(my.cluster1$cluster$label, my.cluster1$cluster$group)
#>           
#>             1  2  3  4  5
#>   outlier3  1  1  1  0  0
#>   pop1      0  0  0  0 50
#>   pop2      0  0  0 50  0

The output directory will be indicated in the console or in my.cluster1$output.dir. All result files are saved at:You can naviage to check the html visualizations in the output directory.

print(my.cluster1$output.dir)
#> [1] "/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmp45z1n6/cluster_output"

list.files(my.cluster1$output.dir)
#> [1] "groups.txt"                "images"                   
#> [3] "RData"                     "tree_scatter_cluster.html"
#> [5] "tree_scatter_label.html"   "tree_scree.html"          
#> [7] "tree_text.html"

About

  • Prof. Kristel Van Steen, visit
  • Kridsadakorn Chaichoompu, visit

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