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lcolladotor/ouptut

Created October 7, 2014 16:10
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purl-derfinder
Raw
ouptut
> library('knitr')
> purl('derfinder.Rmd')
processing file: derfinder.Rmd
|...... | 9%Error in eval(expr, envir, enclos) : object 'windowsFlag' not found
|....... | 11%Error in eval(expr, envir, enclos) : object 'windowsFlag' not found
|.................................................................| 100%
output file: derfinder.R
[1] "derfinder.R"
> library(derfinderData)
> source('derfinder.R')
Writing 30 Bibtex entries ... OK
Results written to file 'derfinderRef.bib'
<table>
<thead>
<tr>
<th align="left"> </th>
<th align="left"> gender </th>
<th align="left"> lab </th>
<th align="right"> Age </th>
<th align="left"> group </th>
</tr>
</thead>
<tbody>
<tr>
<td align="left"> 1 </td>
<td align="left"> F </td>
<td align="left"> HSB97.AMY </td>
<td align="right"> -0.5476190 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 2 </td>
<td align="left"> M </td>
<td align="left"> HSB92.AMY </td>
<td align="right"> -0.4523810 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 3 </td>
<td align="left"> M </td>
<td align="left"> HSB178.AMY </td>
<td align="right"> -0.5714286 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 4 </td>
<td align="left"> M </td>
<td align="left"> HSB159.AMY </td>
<td align="right"> -0.3809524 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 5 </td>
<td align="left"> F </td>
<td align="left"> HSB153.AMY </td>
<td align="right"> -0.6666667 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 6 </td>
<td align="left"> F </td>
<td align="left"> HSB113.AMY </td>
<td align="right"> -0.6666667 </td>
<td align="left"> fetal </td>
</tr>
<tr>
<td align="left"> 7 </td>
<td align="left"> F </td>
<td align="left"> HSB130.AMY </td>
<td align="right"> 21.0000000 </td>
<td align="left"> adult </td>
</tr>
<tr>
<td align="left"> 8 </td>
<td align="left"> M </td>
<td align="left"> HSB136.AMY </td>
<td align="right"> 23.0000000 </td>
<td align="left"> adult </td>
</tr>
<tr>
<td align="left"> 9 </td>
<td align="left"> F </td>
<td align="left"> HSB126.AMY </td>
<td align="right"> 30.0000000 </td>
<td align="left"> adult </td>
</tr>
<tr>
<td align="left"> 10 </td>
<td align="left"> M </td>
<td align="left"> HSB145.AMY </td>
<td align="right"> 36.0000000 </td>
<td align="left"> adult </td>
</tr>
<tr>
<td align="left"> 11 </td>
<td align="left"> M </td>
<td align="left"> HSB123.AMY </td>
<td align="right"> 37.0000000 </td>
<td align="left"> adult </td>
</tr>
<tr>
<td align="left"> 12 </td>
<td align="left"> F </td>
<td align="left"> HSB135.AMY </td>
<td align="right"> 40.0000000 </td>
<td align="left"> adult </td>
</tr>
</tbody>
</table>
2014-10-07 12:02:25 fullCoverage: processing chromosome chr21
2014-10-07 12:02:25 loadCoverage: finding chromosome lengths
2014-10-07 12:02:26 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB113.bw
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 object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: stats4
2014-10-07 12:02:26 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB123.bw
2014-10-07 12:02:26 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB126.bw
2014-10-07 12:02:27 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB130.bw
2014-10-07 12:02:27 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB135.bw
2014-10-07 12:02:27 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB136.bw
2014-10-07 12:02:28 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB145.bw
2014-10-07 12:02:28 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB153.bw
2014-10-07 12:02:28 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB159.bw
2014-10-07 12:02:29 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB178.bw
2014-10-07 12:02:29 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB92.bw
2014-10-07 12:02:29 loadCoverage: loading BigWig file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinderData/extdata/AMY/HSB97.bw
2014-10-07 12:02:30 loadCoverage: applying the cutoff to the merged data
2014-10-07 12:02:30 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered.
2014-10-07 12:02:31 filterData: originally there were 48129895 rows, now there are 130356 rows. Meaning that 99.73 percent was filtered.
2014-10-07 12:02:31 sampleDepth: Calculating sample quantiles
2014-10-07 12:02:37 sampleDepth: Calculating sample adjustments
2014-10-07 12:02:38 analyzeChr: Pre-processing the coverage data
2014-10-07 12:02:44 analyzeChr: Calculating statistics
2014-10-07 12:02:44 calculateStats: calculating the F-statistics
2014-10-07 12:02:44 analyzeChr: Calculating pvalues
2014-10-07 12:02:44 analyzeChr: Using the following theoretical cutoff for the F-statistics 5.31765507157871
2014-10-07 12:02:44 calculatePvalues: identifying data segments
2014-10-07 12:02:44 findRegions: segmenting F-stats information
2014-10-07 12:02:44 findRegions: identifying candidate DERs
2014-10-07 12:02:44 findRegions: identifying DER clusters
2014-10-07 12:02:47 calculatePvalues: calculating F-statistics for permutation 1 and seed 20140924
2014-10-07 12:02:47 findRegions: segmenting F-stats information
2014-10-07 12:02:47 findRegions: identifying candidate DERs
2014-10-07 12:02:47 calculatePvalues: calculating F-statistics for permutation 2 and seed 20140925
2014-10-07 12:02:47 findRegions: segmenting F-stats information
2014-10-07 12:02:47 findRegions: identifying candidate DERs
2014-10-07 12:02:47 calculatePvalues: calculating F-statistics for permutation 3 and seed 20140926
2014-10-07 12:02:48 findRegions: segmenting F-stats information
2014-10-07 12:02:48 findRegions: identifying candidate DERs
2014-10-07 12:02:48 calculatePvalues: calculating F-statistics for permutation 4 and seed 20140927
2014-10-07 12:02:48 findRegions: segmenting F-stats information
2014-10-07 12:02:48 findRegions: identifying candidate DERs
2014-10-07 12:02:48 calculatePvalues: calculating F-statistics for permutation 5 and seed 20140928
2014-10-07 12:02:49 findRegions: segmenting F-stats information
2014-10-07 12:02:49 findRegions: identifying candidate DERs
2014-10-07 12:02:49 calculatePvalues: calculating F-statistics for permutation 6 and seed 20140929
2014-10-07 12:02:49 findRegions: segmenting F-stats information
2014-10-07 12:02:49 findRegions: identifying candidate DERs
2014-10-07 12:02:49 calculatePvalues: calculating F-statistics for permutation 7 and seed 20140930
2014-10-07 12:02:50 findRegions: segmenting F-stats information
2014-10-07 12:02:50 findRegions: identifying candidate DERs
2014-10-07 12:02:50 calculatePvalues: calculating F-statistics for permutation 8 and seed 20140931
2014-10-07 12:02:50 findRegions: segmenting F-stats information
2014-10-07 12:02:50 findRegions: identifying candidate DERs
2014-10-07 12:02:50 calculatePvalues: calculating F-statistics for permutation 9 and seed 20140932
2014-10-07 12:02:50 findRegions: segmenting F-stats information
2014-10-07 12:02:50 findRegions: identifying candidate DERs
2014-10-07 12:02:50 calculatePvalues: calculating F-statistics for permutation 10 and seed 20140933
2014-10-07 12:02:51 findRegions: segmenting F-stats information
2014-10-07 12:02:51 findRegions: identifying candidate DERs
2014-10-07 12:02:51 calculatePvalues: calculating F-statistics for permutation 11 and seed 20140934
2014-10-07 12:02:51 findRegions: segmenting F-stats information
2014-10-07 12:02:51 findRegions: identifying candidate DERs
2014-10-07 12:02:51 calculatePvalues: calculating F-statistics for permutation 12 and seed 20140935
2014-10-07 12:02:51 findRegions: segmenting F-stats information
2014-10-07 12:02:51 findRegions: identifying candidate DERs
2014-10-07 12:02:51 calculatePvalues: calculating F-statistics for permutation 13 and seed 20140936
2014-10-07 12:02:52 findRegions: segmenting F-stats information
2014-10-07 12:02:52 findRegions: identifying candidate DERs
2014-10-07 12:02:52 calculatePvalues: calculating F-statistics for permutation 14 and seed 20140937
2014-10-07 12:02:52 findRegions: segmenting F-stats information
2014-10-07 12:02:52 findRegions: identifying candidate DERs
2014-10-07 12:02:52 calculatePvalues: calculating F-statistics for permutation 15 and seed 20140938
2014-10-07 12:02:53 findRegions: segmenting F-stats information
2014-10-07 12:02:53 findRegions: identifying candidate DERs
2014-10-07 12:02:53 calculatePvalues: calculating F-statistics for permutation 16 and seed 20140939
2014-10-07 12:02:53 findRegions: segmenting F-stats information
2014-10-07 12:02:53 findRegions: identifying candidate DERs
2014-10-07 12:02:53 calculatePvalues: calculating F-statistics for permutation 17 and seed 20140940
2014-10-07 12:02:54 findRegions: segmenting F-stats information
2014-10-07 12:02:54 findRegions: identifying candidate DERs
2014-10-07 12:02:54 calculatePvalues: calculating F-statistics for permutation 18 and seed 20140941
2014-10-07 12:02:54 findRegions: segmenting F-stats information
2014-10-07 12:02:54 findRegions: identifying candidate DERs
2014-10-07 12:02:54 calculatePvalues: calculating F-statistics for permutation 19 and seed 20140942
2014-10-07 12:02:54 findRegions: segmenting F-stats information
2014-10-07 12:02:54 findRegions: identifying candidate DERs
2014-10-07 12:02:54 calculatePvalues: calculating F-statistics for permutation 20 and seed 20140943
2014-10-07 12:02:55 findRegions: segmenting F-stats information
2014-10-07 12:02:55 findRegions: identifying candidate DERs
2014-10-07 12:02:55 calculatePvalues: calculating the p-values
2014-10-07 12:02:58 analyzeChr: Annotating regions
Matching regions to genes.
nearestgene: loading bumphunter hg19 transcript database
finding nearest transcripts...
Annotating.Done.
2014-10-07 12:04:09 mergeResults: Saving options used
2014-10-07 12:04:09 Loading chromosome chr21
2014-10-07 12:04:09 mergeResults: calculating FWER
2014-10-07 12:04:09 mergeResults: Saving fullNullSummary
2014-10-07 12:04:09 mergeResults: Re-calculating the p-values
2014-10-07 12:04:09 mergeResults: Saving fullRegions
2014-10-07 12:04:09 mergeResults: assigning genomic states
2014-10-07 12:04:09 annotateRegions: counting
2014-10-07 12:04:09 annotateRegions: annotating
2014-10-07 12:04:10 mergeResults: Saving fullAnnotatedRegions
2014-10-07 12:04:10 mergeResults: Saving fullFstats
2014-10-07 12:04:10 mergeResults: Saving fullTime
2014-10-07 12:04:10 annotateRegions: counting
2014-10-07 12:04:10 annotateRegions: annotating
2014-10-07 12:04:10 getRegionCoverage: processing chr21
2014-10-07 12:04:11 getRegionCoverage: done processing chr21
2014-10-07 12:04:11 regionMatrix: processing chr21
2014-10-07 12:04:11 filterData: normalizing coverage
2014-10-07 12:04:12 filterData: done normalizing coverage
2014-10-07 12:04:14 filterData: originally there were 48129895 rows, now there are 189651 rows. Meaning that 99.61 percent was filtered.
2014-10-07 12:04:14 findRegions: identifying potential segments
2014-10-07 12:04:14 findRegions: segmenting F-stats information
2014-10-07 12:04:14 findRegions: identifying candidate DERs
2014-10-07 12:04:14 findRegions: identifying DER clusters
2014-10-07 12:04:17 getRegionCoverage: processing chr21
2014-10-07 12:04:18 getRegionCoverage: done processing chr21
2014-10-07 12:04:23 coverageToExon: processing chromosome chr21
2014-10-07 12:04:28 coverageToExon: processing chromosome chr21
2014-10-07 12:04:31 annotateRegions: counting
2014-10-07 12:04:32 annotateRegions: annotating
Matching regions to genes.
nearestgene: loading bumphunter hg19 transcript database
finding nearest transcripts...
Annotating.Done.
2014-10-07 12:05:52 coerceGR: coercing sample HSB97
2014-10-07 12:05:52 createBwSample: exporting bw for sample HSB97
There were 11 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In citation("knitcitations") :
no date field in DESCRIPTION file of package ‘knitcitations’
2: In citation("GenomeInfoDb") :
no date field in DESCRIPTION file of package ‘GenomeInfoDb’
3: In citation("biovizBase") :
no date field in DESCRIPTION file of package ‘biovizBase’
4: In citation("bumphunter") :
no date field in DESCRIPTION file of package ‘bumphunter’
5: In citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
no date field in DESCRIPTION file of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
6: In citation("AnnotationDbi") :
no date field in DESCRIPTION file of package ‘AnnotationDbi’
7: In citation("BiocParallel") :
no date field in DESCRIPTION file of package ‘BiocParallel’
8: In citation("GenomicFiles") :
no date field in DESCRIPTION file of package ‘GenomicFiles’
9: In citation("qvalue") : no date field in DESCRIPTION file of package ‘qvalue’
10: In citation("Rsamtools") :
no date field in DESCRIPTION file of package ‘Rsamtools’
11: In citation("S4Vectors") :
no date field in DESCRIPTION file of package ‘S4Vectors’
> options(width = 90)
> devtools::session_info()
Session info-----------------------------------------------------------------------------
setting value
version R version 3.1.1 (2014-07-10)
system x86_64, darwin10.8.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/New_York
Packages---------------------------------------------------------------------------------
package * version date source
acepack 1.3.3.3 2013-05-03 CRAN (R 3.1.0)
AnnotationDbi 1.27.19 2014-10-05 Bioconductor
base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0)
BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1)
BBmisc 1.7 2014-06-21 CRAN (R 3.1.0)
bibtex 0.3.6 2013-07-29 CRAN (R 3.1.0)
Biobase 2.25.0 2014-04-12 Bioconductor
BiocGenerics * 0.11.5 2014-09-13 Bioconductor
BiocParallel 0.99.25 2014-10-02 Bioconductor
biomaRt 2.21.4 2014-10-02 Bioconductor
Biostrings 2.33.14 2014-09-09 Bioconductor
bitops 1.0.6 2013-08-17 CRAN (R 3.1.0)
brew 1.0.6 2011-04-13 CRAN (R 3.1.0)
bumphunter * 1.5.5 2014-08-29 Bioconductor
checkmate 1.4 2014-09-03 CRAN (R 3.1.1)
cluster 1.15.3 2014-09-04 CRAN (R 3.1.1)
codetools 0.2.9 2014-08-21 CRAN (R 3.1.1)
colorout * 1.0.2 2014-03-06 local
colorspace 1.2.4 2013-09-30 CRAN (R 3.1.0)
DBI 0.3.1 2014-09-24 CRAN (R 3.1.1)
derfinder * 0.99.5 2014-09-30 Github (lcolladotor/derfinder@da289c4)
derfinderData * 0.99.1 2014-09-30 Github (lcolladotor/derfinderData@cab813f)
derfinderHelper 0.99.2 2014-09-29 Github (lcolladotor/derfinderHelper@54a9721)
devtools * 1.6 2014-09-23 CRAN (R 3.1.1)
digest 0.6.4 2013-12-03 CRAN (R 3.1.0)
doRNG 1.6 2014-03-07 CRAN (R 3.1.1)
evaluate 0.5.5 2014-04-29 CRAN (R 3.1.0)
fail 1.2 2013-09-19 CRAN (R 3.1.0)
foreach * 1.4.2 2014-04-11 CRAN (R 3.1.0)
foreign 0.8.61 2014-03-28 CRAN (R 3.1.0)
formatR 1.0 2014-08-25 CRAN (R 3.1.1)
Formula 1.1.2 2014-07-13 CRAN (R 3.1.1)
futile.logger 1.3.7 2014-01-23 CRAN (R 3.1.0)
futile.options 1.0.0 2010-04-06 CRAN (R 3.1.0)
GenomeInfoDb * 1.1.25 2014-10-02 Bioconductor
GenomicAlignments 1.1.30 2014-09-23 Bioconductor
GenomicFeatures 1.17.19 2014-10-01 Bioconductor
GenomicFiles 1.1.19 2014-08-26 Bioconductor
GenomicRanges * 1.17.43 2014-10-02 Bioconductor
ggplot2 * 1.0.0 2014-05-21 CRAN (R 3.1.0)
gtable 0.1.2 2012-12-05 CRAN (R 3.1.0)
Hmisc 3.14.5 2014-09-12 CRAN (R 3.1.1)
httr 0.5 2014-09-02 CRAN (R 3.1.1)
IRanges * 1.99.30 2014-10-05 Bioconductor
iterators * 1.0.7 2014-04-11 CRAN (R 3.1.0)
knitcitations * 1.0.2 2014-09-30 Github (cboettig/knitcitations@f567713)
knitr * 1.6 2014-05-25 CRAN (R 3.1.0)
lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.0)
lattice 0.20.29 2014-04-04 CRAN (R 3.1.0)
latticeExtra 0.6.26 2013-08-15 CRAN (R 3.1.0)
locfit * 1.5.9.1 2013-04-20 CRAN (R 3.1.0)
lubridate 1.3.3 2013-12-31 CRAN (R 3.1.0)
MASS 7.3.35 2014-09-30 CRAN (R 3.1.1)
Matrix 1.1.4 2014-06-15 CRAN (R 3.1.0)
matrixStats 0.10.0 2014-06-08 CRAN (R 3.1.0)
memoise 0.2.1 2014-04-22 CRAN (R 3.1.0)
munsell 0.4.2 2013-07-11 CRAN (R 3.1.0)
nnet 7.3.8 2014-03-28 CRAN (R 3.1.0)
pkgmaker 0.22 2014-05-14 CRAN (R 3.1.0)
plyr 1.8.1 2014-02-26 CRAN (R 3.1.0)
proto 0.3.10 2012-12-22 CRAN (R 3.1.0)
qvalue 1.39.1 2014-05-27 Bioconductor
R.methodsS3 1.6.1 2014-01-05 CRAN (R 3.1.0)
RColorBrewer 1.0.5 2011-06-17 CRAN (R 3.1.0)
Rcpp 0.11.3 2014-09-29 CRAN (R 3.1.1)
RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1)
RefManageR 0.8.34 2014-08-19 CRAN (R 3.1.1)
registry 0.2 2012-01-24 CRAN (R 3.1.0)
reshape2 1.4 2014-04-23 CRAN (R 3.1.0)
RJSONIO 1.3.0 2014-07-28 CRAN (R 3.1.1)
rngtools 1.2.4 2014-03-06 CRAN (R 3.1.0)
rpart 4.1.8 2014-03-28 CRAN (R 3.1.0)
Rsamtools 1.17.34 2014-09-20 Bioconductor
RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0)
rstudioapi 0.1 2014-03-27 CRAN (R 3.1.0)
rtracklayer 1.25.19 2014-10-02 Bioconductor
S4Vectors * 0.2.4 2014-09-14 Bioconductor
scales 0.2.4 2014-04-22 CRAN (R 3.1.0)
sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1)
stringr 0.6.2 2012-12-06 CRAN (R 3.1.0)
survival 2.37.7 2014-01-22 CRAN (R 3.1.0)
XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
xtable 1.7.4 2014-09-12 CRAN (R 3.1.1)
XVector 0.5.8 2014-09-07 Bioconductor
zlibbioc 1.11.1 2014-04-19 Bioconductor
>
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