R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(deepSNV)
Loading required package: parallel
Loading required package: Rhtslib
Rhtslib htslib version 1.1
Loading required package: IRanges
Loading required package: BiocGenerics
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.
Loading required package: Biostrings
Loading required package: XVector
Loading required package: VGAM
Loading required package: splines
Loading required package: VariantAnnotation
Loading required package: Rsamtools
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Attaching package: 'deepSNV'
The following objects are masked from 'package:VGAM':
dbetabinom, pbetabinom
The following object is masked from 'package:BiocGenerics':
normalize
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/deepSNV/RCC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RCC
> ### Title: Example RCC data
> ### Aliases: RCC
>
> ### ** Examples
>
> data("RCC", package="deepSNV")
> summary(RCC, adjust.method="bonferroni")[,1:6]
chr pos ref var p.val freq.var
6 chr10 89710231 C T 1.812318e-06 -0.0522069105
1 chr17 7512879 G A 4.923709e-03 0.0095680379
10 chr17 7513782 A G 6.137099e-57 0.0523098637
15 chr3 10158255 A - 7.414419e-27 0.0374605077
4 chr3 10158274 C T 6.596999e-152 -0.1420210172
2 chr3 10158337 G A 8.455105e-09 -0.1458150689
7 chr3 10163012 - C 2.512916e-211 0.1242571351
16 chr3 10163206 T - 0.000000e+00 0.2440387988
17 chr3 10163208 G - 1.908223e-02 0.0007724394
11 chr3 10163428 T G 1.026389e-79 -0.1111055718
8 chr3 10166219 G C 6.538408e-74 0.1591560973
3 chr3 10166943 G A 1.406981e-158 -0.1326056510
12 chr3 10167220 C G 2.960126e-36 0.0046531880
13 chr3 10167672 A G 0.000000e+00 0.1399833662
5 chr3 10167709 C T 6.203881e-304 -0.1440968910
9 chr3 10167762 T C 0.000000e+00 -0.1323353964
14 chr3 10168683 T G 2.134656e-304 -0.1324914089
> plot(RCC)
> RCC.bb <- estimateDispersion(RCC, alternative="two.sided")
Note: The initial object used a binomial model. Will be changed to beta-binomial.
Estimated dispersion factor 136.926849574802
> summary(RCC.bb, adjust.method="bonferroni")[,1:6]
chr pos ref var p.val freq.var
2 chr3 10158274 C T 4.185487e-03 -0.1420210172
7 chr3 10163206 T - 6.777322e-304 0.2440387988
8 chr3 10163208 G - 2.693887e-02 0.0007724394
1 chr3 10166943 G A 9.500067e-03 -0.1326056510
5 chr3 10167220 C G 5.461071e-30 0.0046531880
3 chr3 10167709 C T 3.466478e-02 -0.1440968910
4 chr3 10167762 T C 8.715720e-03 -0.1323353964
6 chr3 10168683 T G 4.237396e-02 -0.1324914089
> plot(RCC.bb)
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>
>
>
>
> dev.off()
null device
1
>