This page was generated on 2018-04-12 13:11:24 -0400 (Thu, 12 Apr 2018).
SeqVarTools 1.16.1 Stephanie M. Gogarten , Xiuwen Zheng , Adrienne Stilp
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/SeqVarTools |
Branch: RELEASE_3_6 |
Last Commit: eea11aa |
Last Changed Date: 2018-03-16 21:12:27 -0400 (Fri, 16 Mar 2018) |
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R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
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> library(GenomicRanges)
Loading required package: stats4
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
> BiocGenerics:::testPackage("SeqVarTools")
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
# of selected samples: 5
# of selected variants: 5
# of selected samples: 85
# of selected variants: 9
# of selected samples: 5
# of selected variants: 5
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 non-overlapping variant matches identified!
# of selected samples: 2
# of selected variants: 1,346
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 non-overlapping variant matches identified!
# of selected variants: 26
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
File: /home/biocbuild/bbs-3.6-bioc/R/library/SeqArray/extdata/CEU_Exon.gds (298.6K)
+ [ ] *
|--+ description [ ] *
|--+ sample.id { Str8 90 LZMA_ra(35.8%), 258B } *
|--+ variant.id { Int32 1348 LZMA_ra(16.8%), 906B } *
|--+ position { Int32 1348 LZMA_ra(64.6%), 3.4K } *
|--+ chromosome { Str8 1348 LZMA_ra(4.63%), 158B } *
|--+ allele { Str8 1348 LZMA_ra(16.7%), 902B } *
|--+ genotype [ ] *
| |--+ data { Bit2 2x90x1348 LZMA_ra(26.3%), 15.6K } *
| |--+ ˜data { Bit2 2x1348x90 LZMA_ra(29.3%), 17.3K }
| |--+ extra.index { Int32 3x0 LZMA_ra, 19B } *
| \--+ extra { Int16 0 LZMA_ra, 19B }
|--+ phase [ ]
| |--+ data { Bit1 90x1348 LZMA_ra(0.91%), 138B } *
| |--+ ˜data { Bit1 1348x90 LZMA_ra(0.91%), 138B }
| |--+ extra.index { Int32 3x0 LZMA_ra, 19B } *
| \--+ extra { Bit1 0 LZMA_ra, 19B }
|--+ annotation [ ]
| |--+ id { Str8 1348 LZMA_ra(38.4%), 5.5K } *
| |--+ qual { Float32 1348 LZMA_ra(2.26%), 122B } *
| |--+ filter { Int32,factor 1348 LZMA_ra(2.26%), 122B } *
| |--+ info [ ]
| | |--+ AA { Str8 1348 LZMA_ra(25.6%), 690B } *
| | |--+ AC { Int32 1348 LZMA_ra(24.2%), 1.3K } *
| | |--+ AN { Int32 1348 LZMA_ra(19.8%), 1.0K } *
| | |--+ DP { Int32 1348 LZMA_ra(47.9%), 2.5K } *
| | |--+ HM2 { Bit1 1348 LZMA_ra(150.3%), 254B } *
| | |--+ HM3 { Bit1 1348 LZMA_ra(150.3%), 254B } *
| | |--+ OR { Str8 1348 LZMA_ra(20.1%), 342B } *
| | |--+ GP { Str8 1348 LZMA_ra(24.4%), 3.8K } *
| | \--+ BN { Int32 1348 LZMA_ra(20.9%), 1.1K } *
| \--+ format [ ]
| \--+ DP [ ] *
| |--+ data { Int32 90x1348 LZMA_ra(25.1%), 118.8K } *
| \--+ ˜data { Int32 1348x90 LZMA_ra(24.1%), 114.2K }
\--+ sample.annotation [ ]
\--+ family { Str8 90 LZMA_ra(57.1%), 222B }
# of selected variants: 142
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 5
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 5
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
# of selected variants: 26
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
# of selected variants: 26
# of selected samples: 4
# of selected variants: 10
subject 1 of 2
subject 2 of 2
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 10
subject 1 of 2
subject 2 of 2
Warning in SeqVarTools:::.samplePairs(samples) :
More than two samples for subject 4
Selecting first two samples: samp7, samp8
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected variants: 1,346
# of selected variants: 1,330
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 3
# of selected variants: 10
# of selected samples: 3
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 10
# of selected samples: 3
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected variants: 903
# of selected samples: 64
# of selected samples: 66
# of selected samples: 24
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 10
# of selected samples: 10
# of selected variants: 10
# of selected samples: 10
RUNIT TEST PROTOCOL -- Thu Apr 12 02:56:32 2018
***********************************************
Number of test functions: 129
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqVarTools RUnit Tests - 129 test functions, 0 errors, 0 failures
Number of test functions: 129
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
53.760 0.276 54.110