This page was generated on 2018-04-12 13:13:23 -0400 (Thu, 12 Apr 2018).
GENESIS 2.8.1 Matthew P. Conomos , Stephanie M. Gogarten
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/GENESIS |
Branch: RELEASE_3_6 |
Last Commit: 9a4284c |
Last Changed Date: 2018-01-18 16:19:04 -0400 (Thu, 18 Jan 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> BiocGenerics:::testPackage("GENESIS")
Loading required package: SeqArray
Loading required package: gdsfmt
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'GWASTools'
The following objects are masked from 'package:SeqVarTools':
alleleFrequency, duplicateDiscordance, getGenotype, mendelErr
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
# of selected variants: 100
# of selected samples: 90
# of selected variants: 1,348
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Reading in Phenotype and Covariate Data...
Fitting Model with 90 Samples
Loading required namespace: survey
Loading required namespace: CompQuadForm
Reading .kin0 file...
Reading .kin file...
Determining Unique Individual IDs from KING Output...
Checking Provided Individual IDs
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 5.956 secs
...SNP Block 2 of 2 Completed - 4.917 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 4.877 secs
...SNP Block 2 of 2 Completed - 5.422 secs
Performing Small Sample Correction...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.4279 secs
...SNP Block 2 of 2 Completed - 0.7239 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 4.848 secs
...SNP Block 2 of 2 Completed - 5.4 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.7354 secs
...SNP Block 2 of 2 Completed - 0.4292 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 6.029 secs
...SNP Block 2 of 2 Completed - 4.961 secs
Performing Small Sample Correction...
RUNIT TEST PROTOCOL -- Wed Apr 11 23:50:51 2018
***********************************************
Number of test functions: 26
Number of errors: 0
Number of failures: 0
1 Test Suite :
GENESIS RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
89.248 0.752 90.733