Aaron Lun
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/diffHic |
| Branch: RELEASE_3_6 |
| Last Commit: c526392 |
| Last Changed Date: 2017-10-30 12:40:51 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:40:54 -0400 (Thu, 12 Apr 2018).
| Package 365/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffHic 1.10.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: diffHic |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.10.0.tar.gz |
| StartedAt: 2018-04-12 02:52:21 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:59:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 429.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffHic.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/diffHic.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘diffHic’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeCNV 10.207 0.08 10.442
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
diffHic.Rcheck/00install.out
* installing *source* package ‘diffHic’ ... ** libs clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c binner.cpp -o binner.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c check_input.cpp -o check_input.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cluster_2d.cpp -o cluster_2d.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c count_background.cpp -o count_background.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c count_connect.cpp -o count_connect.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c count_patch.cpp -o count_patch.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c directionality.cpp -o directionality.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c iterative_correction.cpp -o iterative_correction.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c neighbors.cpp -o neighbors.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c pair_stats.cpp -o pair_stats.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c quadrant_bg.cpp -o quadrant_bg.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c report_hic_pairs.cpp -o report_hic_pairs.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c trended_filter.cpp -o trended_filter.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o utils.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] installing to /Users/biocbuild/bbs-3.6-bioc/meat/diffHic.Rcheck/diffHic/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (diffHic)
diffHic.Rcheck/tests/test-basic.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # These are just placeholders for the real things in inst/tests.
>
> suppressWarnings(suppressPackageStartupMessages(require(diffHic)))
>
> hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
> cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
> param <- pairParam(fragments=cuts)
>
> # Setting up the parameters
> fout <- "output.h5"
> preparePairs(hic.file, param, file=fout)
$pairs
total marked filtered mapped
32 7 3 22
$same.id
dangling self.circle
4 1
$singles
[1] 2
$chimeras
total mapped multi invalid
12 8 7 5
> head(getPairData(fout, param))
length orientation insert
1 40 1 40
2 80 1 80
3 60 2 54
4 40 3 160
5 20 1 66
6 80 0 114
>
> loadChromos(fout)
anchor1 anchor2
1 chrA chrA
2 chrB chrA
3 chrB chrB
> head(loadData(fout, "chrA", "chrA"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 2 1 49 14 -5 10
2 2 1 79 9 -10 10
3 2 1 65 21 10 -10
4 4 1 156 6 -10 -10
5 4 2 141 80 -5 10
6 4 2 154 50 10 10
> head(loadData(fout, "chrA", "chrB"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 5 2 19 44 10 -10
2 5 3 14 105 10 -10
3 6 1 65 19 5 10
4 6 2 24 90 -5 5
5 6 3 24 100 -5 -10
6 6 3 24 95 -5 -10
Warning message:
In value[[3L]](cond) : anchor definitions are reversed
>
> # Loading the counts.
> data <- squareCounts(fout, param, width=50, filter=1)
> data
class: InteractionSet
dim: 10 1
metadata(2): param width
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
>
> margins <- marginCounts(fout, param, width=50)
> margins
class: RangedSummarizedExperiment
dim: 6 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(1): nfrags
colnames: NULL
colData names(1): totals
> totalCounts(fout, param)
[1] 17
>
> regions <- GRanges("chrA", IRanges(c(1, 100, 150), c(20, 140, 160)))
> connectCounts(fout, param, regions=regions, filter=1L)
class: InteractionSet
dim: 2 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 3
>
> # Checking some values.
> head(getArea(data))
[1] 2208 2304 2208 2208 3312 3174
> head(pairdist(data))
[1] 47 140 93 47 NA NA
>
> anchors(data, type="first")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 49, 94] * | 1
[2] chrA [141, 188] * | 1
[3] chrA [141, 188] * | 1
[4] chrA [141, 188] * | 1
[5] chrB [ 1, 69] * | 2
[6] chrB [ 1, 69] * | 2
[7] chrB [ 1, 69] * | 2
[8] chrB [ 1, 69] * | 2
[9] chrB [ 70, 92] * | 1
[10] chrB [ 70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> anchors(data, type="second")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 1, 48] * | 1
[2] chrA [ 1, 48] * | 1
[3] chrA [49, 94] * | 1
[4] chrA [95, 140] * | 1
[5] chrA [ 1, 48] * | 1
[6] chrA [49, 94] * | 1
[7] chrA [95, 140] * | 1
[8] chrB [ 1, 69] * | 2
[9] chrB [ 1, 69] * | 2
[10] chrB [70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> assay(data)
[,1]
[1,] 3
[2,] 1
[3,] 2
[4,] 1
[5,] 1
[6,] 2
[7,] 3
[8,] 1
[9,] 2
[10,] 1
> regions(data)
GRanges object with 6 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 1, 48] * | 1
[2] chrA [ 49, 94] * | 1
[3] chrA [ 95, 140] * | 1
[4] chrA [141, 188] * | 1
[5] chrB [ 1, 69] * | 2
[6] chrB [ 70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
>
> data$totals
[1] 17
> colData(data)
DataFrame with 1 row and 1 column
totals
<integer>
1 17
> metadata(data)
$param
Genome contains 7 restriction fragments across 2 chromosomes
No discard regions are specified
No limits on chromosomes for read extraction
No cap on the read pairs per pair of restriction fragments
$width
[1] 50
>
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1
1 3
2 1
3 2
4 1
5 1
6 2
7 3
8 1
9 2
10 1
$samples
group lib.size norm.factors
Sample1 1 17 1
> asDGEList(data, lib.size=20)$samples
group lib.size norm.factors
Sample1 1 20 1
> asDGEList(data, norm.factors=2, group="a")$samples
group lib.size norm.factors
Sample1 a 17 2
>
> # Simple normalization with dummy data.
> set.seed(3423746)
> npts <- 100
> npairs <- 5000
> nlibs <- 4
> anchors <- sample(npts, npairs, replace=TRUE)
> targets <- sample(npts, npairs, replace=TRUE)
> dummy <- InteractionSet(matrix(as.integer(rpois(npairs*nlibs, runif(npairs, 10, 100))), nrow=npairs),
+ colData=DataFrame(totals=runif(nlibs, 1e6, 2e6)),
+ GInteractions(anchor1=anchors, anchor2=targets, regions=GRanges("chrA", IRanges(1:npts, 1:npts)), mode="reverse"))
>
> normOffsets(dummy, se.out=FALSE)
[1] 1.0797833 0.8315381 0.9929250 1.1216692
> normOffsets(dummy, logratioTrim=0, se.out=FALSE)
[1] 1.0811625 0.8302084 0.9910453 1.1241607
> normOffsets(dummy, sumTrim=0.2, se.out=FALSE)
[1] 1.0809185 0.8315821 0.9932535 1.1200614
> head(normOffsets(dummy, type="loess", se.out=FALSE))
[,1] [,2] [,3] [,4]
[1,] -0.001441205 0.0009288925 0.004926866 -0.004414553
[2,] 0.005400642 0.0041595535 -0.006896159 -0.002664036
[3,] 0.003115172 -0.0016344146 0.001783304 -0.003264061
[4,] 0.005334705 0.0035367018 -0.005104467 -0.003766940
[5,] -0.003505626 0.0163064598 -0.001889796 -0.010911038
[6,] 0.004070281 0.0090487722 -0.008279823 -0.004839230
> head(normOffsets(dummy, type="loess", span=0.5, se.out=FALSE))
[,1] [,2] [,3] [,4]
[1,] -0.0024209802 0.0006743114 0.003720243 -0.0019735742
[2,] 0.0063348094 0.0041435451 -0.006281532 -0.0041968230
[3,] -0.0009160654 -0.0004010371 0.002050126 -0.0007330237
[4,] 0.0067668226 0.0036523870 -0.005981149 -0.0044380604
[5,] -0.0016877799 0.0152247018 -0.006733298 -0.0068036242
[6,] 0.0031066311 0.0085339697 -0.006865167 -0.0047754340
>
> # Playing around with some bin counts.
> stuff <- correctedContact(data)
> head(stuff$truth)
[1] 1.517032e+04 6.123523e-01 6.123523e-01 8.162749e-01 2.041633e-01
[6] 2.041633e-01
>
> data.large <- squareCounts(fout, param, width=100, filter=1)
> boxed <- boxPairs(larger=data.large, smaller=data)
> head(boxed$indices$larger)
[1] 1 2 3 4 5 6
> head(boxed$indices$smaller)
[1] 1 2 2 3 4 4
>
> head(enrichedPairs(data))
class: InteractionSet
dim: 6 1
metadata(2): param width
assays(5): counts quadrant vertical horizontal surrounding
rownames: NULL
rowData names(4): N.quadrant N.vertical N.horizontal N.surrounding
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
> head(clusterPairs(data, tol=10)$indices[[1]])
[1] 1 2 2 2 3 3
>
> # End.
>
> unlink(fout)
>
> proc.time()
user system elapsed
15.075 0.405 15.706
diffHic.Rcheck/tests/test-basic.Rout.save
R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # These are just placeholders for the real things in inst/tests.
>
> suppressWarnings(suppressPackageStartupMessages(require(diffHic)))
>
> hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
> cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
> param <- pairParam(fragments=cuts)
>
> # Setting up the parameters
> fout <- "output.h5"
> preparePairs(hic.file, param, file=fout)
$pairs
total marked filtered mapped
32 7 3 22
$same.id
dangling self.circle
4 1
$singles
[1] 2
$chimeras
total mapped multi invalid
12 8 7 5
> head(getPairData(fout, param))
length orientation insert
1 40 1 40
2 80 1 80
3 60 2 54
4 40 3 160
5 20 1 66
6 80 0 114
>
> loadChromos(fout)
anchor1 anchor2
1 chrA chrA
2 chrB chrA
3 chrB chrB
> head(loadData(fout, "chrA", "chrA"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 2 1 49 14 -5 10
2 2 1 79 9 -10 10
3 2 1 65 21 10 -10
4 4 1 156 6 -10 -10
5 4 2 141 80 -5 10
6 4 2 154 50 10 10
> head(loadData(fout, "chrA", "chrB"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 5 2 19 44 10 -10
2 5 3 14 105 10 -10
3 6 1 65 19 5 10
4 6 2 24 90 -5 5
5 6 3 24 100 -5 -10
6 6 3 24 95 -5 -10
Warning message:
In value[[3L]](cond) : anchor definitions are reversed
>
> # Loading the counts.
> data <- squareCounts(fout, param, width=50, filter=1)
> data
class: InteractionSet
dim: 10 1
metadata(2): param width
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
>
> margins <- marginCounts(fout, param, width=50)
> margins
class: RangedSummarizedExperiment
dim: 6 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(1): nfrags
colnames: NULL
colData names(1): totals
> totalCounts(fout, param)
[1] 17
>
> regions <- GRanges("chrA", IRanges(c(1, 100, 150), c(20, 140, 160)))
> connectCounts(fout, param, regions=regions, filter=1L)
class: InteractionSet
dim: 2 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 3
>
> # Checking some values.
> head(getArea(data))
[1] 2208 2304 2208 2208 3312 3174
> head(pairdist(data))
[1] 47 140 93 47 NA NA
>
> anchors(data, type="first")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 49, 94] * | 1
[2] chrA [141, 188] * | 1
[3] chrA [141, 188] * | 1
[4] chrA [141, 188] * | 1
[5] chrB [ 1, 69] * | 2
[6] chrB [ 1, 69] * | 2
[7] chrB [ 1, 69] * | 2
[8] chrB [ 1, 69] * | 2
[9] chrB [ 70, 92] * | 1
[10] chrB [ 70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> anchors(data, type="second")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 1, 48] * | 1
[2] chrA [ 1, 48] * | 1
[3] chrA [49, 94] * | 1
[4] chrA [95, 140] * | 1
[5] chrA [ 1, 48] * | 1
[6] chrA [49, 94] * | 1
[7] chrA [95, 140] * | 1
[8] chrB [ 1, 69] * | 2
[9] chrB [ 1, 69] * | 2
[10] chrB [70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> assay(data)
[,1]
[1,] 3
[2,] 1
[3,] 2
[4,] 1
[5,] 1
[6,] 2
[7,] 3
[8,] 1
[9,] 2
[10,] 1
> regions(data)
GRanges object with 6 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA [ 1, 48] * | 1
[2] chrA [ 49, 94] * | 1
[3] chrA [ 95, 140] * | 1
[4] chrA [141, 188] * | 1
[5] chrB [ 1, 69] * | 2
[6] chrB [ 70, 92] * | 1
-------
seqinfo: 2 sequences from an unspecified genome
>
> data$totals
[1] 17
> colData(data)
DataFrame with 1 row and 1 column
totals
<integer>
1 17
> metadata(data)
$param
Genome contains 7 restriction fragments across 2 chromosomes
No discard regions are specified
No limits on chromosomes for read extraction
No cap on the read pairs per pair of restriction fragments
$width
[1] 50
>
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1
1 3
2 1
3 2
4 1
5 1
6 2
7 3
8 1
9 2
10 1
$samples
group lib.size norm.factors
Sample1 1 17 1
> asDGEList(data, lib.size=20)$samples
group lib.size norm.factors
Sample1 1 20 1
> asDGEList(data, norm.factors=2, group="a")$samples
group lib.size norm.factors
Sample1 a 17 2
>
> # Simple normalization with dummy data.
> set.seed(3423746)
> npts <- 100
> npairs <- 5000
> nlibs <- 4
> anchors <- sample(npts, npairs, replace=TRUE)
> targets <- sample(npts, npairs, replace=TRUE)
> dummy <- InteractionSet(matrix(as.integer(rpois(npairs*nlibs, runif(npairs, 10, 100))), nrow=npairs),
+ colData=DataFrame(totals=runif(nlibs, 1e6, 2e6)),
+ GInteractions(anchor1=anchors, anchor2=targets, regions=GRanges("chrA", IRanges(1:npts, 1:npts)), mode="reverse"))
>
> normOffsets(dummy, se.out=FALSE)
[1] 1.0797833 0.8315381 0.9929250 1.1216692
> normOffsets(dummy, logratioTrim=0, se.out=FALSE)
[1] 1.0811625 0.8302084 0.9910453 1.1241607
> normOffsets(dummy, sumTrim=0.2, se.out=FALSE)
[1] 1.0809185 0.8315821 0.9932535 1.1200614
> head(normOffsets(dummy, type="loess", se.out=FALSE))
[,1] [,2] [,3] [,4]
[1,] -0.001441205 0.0009288925 0.004926866 -0.004414553
[2,] 0.005400642 0.0041595535 -0.006896159 -0.002664036
[3,] 0.003115172 -0.0016344146 0.001783304 -0.003264061
[4,] 0.005334705 0.0035367018 -0.005104467 -0.003766940
[5,] -0.003505626 0.0163064598 -0.001889796 -0.010911038
[6,] 0.004070281 0.0090487722 -0.008279823 -0.004839230
> head(normOffsets(dummy, type="loess", span=0.5, se.out=FALSE))
[,1] [,2] [,3] [,4]
[1,] -0.0024209802 0.0006743114 0.003720243 -0.0019735742
[2,] 0.0063348094 0.0041435451 -0.006281532 -0.0041968230
[3,] -0.0009160654 -0.0004010371 0.002050126 -0.0007330237
[4,] 0.0067668226 0.0036523870 -0.005981149 -0.0044380604
[5,] -0.0016877799 0.0152247018 -0.006733298 -0.0068036242
[6,] 0.0031066311 0.0085339697 -0.006865167 -0.0047754340
>
> # Playing around with some bin counts.
> stuff <- correctedContact(data)
> head(stuff$truth)
[1] 1.517032e+04 6.123523e-01 6.123523e-01 8.162749e-01 2.041633e-01
[6] 2.041633e-01
>
> data.large <- squareCounts(fout, param, width=100, filter=1)
> boxed <- boxPairs(larger=data.large, smaller=data)
> head(boxed$indices$larger)
[1] 1 2 3 4 5 6
> head(boxed$indices$smaller)
[1] 1 2 2 3 4 4
>
> head(enrichedPairs(data))
class: InteractionSet
dim: 6 1
metadata(2): param width
assays(5): counts quadrant vertical horizontal surrounding
rownames: NULL
rowData names(4): N.quadrant N.vertical N.horizontal N.surrounding
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
> head(clusterPairs(data, tol=10)$indices[[1]])
[1] 1 2 2 2 3 3
>
> # End.
>
> unlink(fout)
>
> proc.time()
user system elapsed
9.875 0.292 10.447
diffHic.Rcheck/diffHic-Ex.timings
| name | user | system | elapsed | |
| DNaseHiC | 0.599 | 0.010 | 0.622 | |
| annotatePairs | 1.017 | 0.005 | 1.043 | |
| boxPairs | 1.412 | 0.011 | 1.442 | |
| clusterPairs | 0.818 | 0.006 | 0.832 | |
| compartmentalize | 0.748 | 0.011 | 0.766 | |
| connectCounts | 1.991 | 0.048 | 2.089 | |
| consolidatePairs | 0.418 | 0.009 | 0.444 | |
| correctedContact | 0.278 | 0.011 | 0.295 | |
| cutGenome | 4.723 | 0.101 | 4.925 | |
| diClusters | 1.262 | 0.024 | 1.305 | |
| diffHicUsersGuide | 0.002 | 0.000 | 0.002 | |
| domainDirections | 0.250 | 0.006 | 0.258 | |
| enrichedPairs | 0.273 | 0.002 | 0.281 | |
| extractPatch | 0.809 | 0.006 | 0.822 | |
| filterDiag | 0.140 | 0.004 | 0.146 | |
| filterPeaks | 0.225 | 0.001 | 0.233 | |
| filters | 0.137 | 0.002 | 0.142 | |
| getArea | 0.181 | 0.003 | 0.186 | |
| getPairData | 0.052 | 0.004 | 0.061 | |
| loadData | 0.063 | 0.005 | 0.069 | |
| marginCounts | 0.652 | 0.008 | 0.666 | |
| mergeCMs | 0.504 | 0.009 | 0.517 | |
| mergePairs | 0.236 | 0.013 | 0.255 | |
| neighborCounts | 0.143 | 0.004 | 0.149 | |
| normalizeCNV | 10.207 | 0.080 | 10.442 | |
| pairParam | 0.115 | 0.001 | 0.124 | |
| plotDI | 0.693 | 0.010 | 0.723 | |
| plotPlaid | 1.644 | 0.017 | 1.697 | |
| preparePairs | 0.230 | 0.025 | 0.263 | |
| prunePairs | 0.212 | 0.016 | 0.229 | |
| savePairs | 0.055 | 0.003 | 0.060 | |
| squareCounts | 0.822 | 0.011 | 0.839 | |
| totalCounts | 0.549 | 0.010 | 0.575 | |