There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to version 2.4.8
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Entering edit mode
Gary ▴ 20
@gary-7967
Last seen 5.7 years ago

Hi,

I would like to use dba.plotVolcano function in DiffBind, but R 3.3.3 cannot find it. In addition, I found that options of bNotDb, bGain, and bLoss for dba.report don’t work in my DiffBind 2.2.12. I guess that it is because my DiffBind is not the last version, i.e. 2.4.8. However, when I install DiffBind again, it is still the 2.2.12 version. Could you help me and please see the detail below.

Best,

Gary

 

R version 3.3.3 (2017-03-06) -- "Another Canoe"

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> require("DiffBind")

Loading required package: DiffBind

Loading required package: 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, xtabs


The following objects are masked from ‘package:base’:


    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,

    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,

    is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste,

    pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,

    sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,

    which.max, which.min


Loading required package: S4Vectors


Attaching package: ‘S4Vectors’


The following objects are masked from ‘package:base’:


    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: IRanges

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")'.


No methods found in "RSQLite" for requests: dbGetQuery

> setwd(system.file("extra", package = "DiffBind"))

> data("tamoxifen_analysis")

> tamoxifen

11 Samples, 2845 sites in matrix:

       ID Tissue Factor  Condition  Treatment Replicate Caller Intervals FRiP

1  BT4741  BT474     ER  Resistant Full-Media         1 counts      2845 0.16

2  BT4742  BT474     ER  Resistant Full-Media         2 counts      2845 0.15

3   MCF71   MCF7     ER Responsive Full-Media         1 counts      2845 0.27

4   MCF72   MCF7     ER Responsive Full-Media         2 counts      2845 0.17

5   MCF73   MCF7     ER Responsive Full-Media         3 counts      2845 0.23

6   T47D1   T47D     ER Responsive Full-Media         1 counts      2845 0.10

7   T47D2   T47D     ER Responsive Full-Media         2 counts      2845 0.06

8  MCF7r1   MCF7     ER  Resistant Full-Media         1 counts      2845 0.20

9  MCF7r2   MCF7     ER  Resistant Full-Media         2 counts      2845 0.13

10  ZR751   ZR75     ER Responsive Full-Media         1 counts      2845 0.32

11  ZR752   ZR75     ER Responsive Full-Media         2 counts      2845 0.22


1 Contrast:

     Group1 Members1     Group2 Members2 DB.DESeq2

1 Resistant        4 Responsive        7       657

> dba.plotPCA(tamoxifen, DBA_TISSUE, label = DBA_CONDITION)

> dba.plotVolcano(tamoxifen)

Error: could not find function "dba.plotVolcano"

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

A new version of Bioconductor is available after installing the most recent version of

  R; see http://bioconductor.org/install

> biocLite("DiffBind")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).

Installing package(s) ‘DiffBind’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/DiffBind_2.2.12.tgz'

Content type 'application/x-gzip' length 2032860 bytes (1.9 MB)

==================================================

downloaded 1.9 MB



The downloaded binary packages are in

/var/folders/rm/tqs8q04d7dg59crpg05pfd1w0000gn/T//Rtmpy19PRb/downloaded_packages

Old packages: 'gdata', 'GGally', 'mgcv', 'RcppArmadillo'

Update all/some/none? [a/s/n]: 

a


  There are binary versions available but the source versions are later:

                   binary      source needs_compilation

mgcv               1.8-18      1.8-19              TRUE

RcppArmadillo 0.7.960.1.1 0.7.960.1.2              TRUE


Do you want to install from sources the packages which need compilation?

y/n: y

trying URL 'https://ftp.yzu.edu.tw/CRAN/bin/macosx/mavericks/contrib/3.3/gdata_2.18.0.tgz'

Content type 'application/octet-stream' length 1141908 bytes (1.1 MB)

==================================================

downloaded 1.1 MB


trying URL 'https://ftp.yzu.edu.tw/CRAN/bin/macosx/mavericks/contrib/3.3/GGally_1.3.2.tgz'

Content type 'application/octet-stream' length 1240773 bytes (1.2 MB)

==================================================

downloaded 1.2 MB



The downloaded binary packages are in

/var/folders/rm/tqs8q04d7dg59crpg05pfd1w0000gn/T//Rtmpy19PRb/downloaded_packages

installing the source packages ‘mgcv’, ‘RcppArmadillo’


trying URL 'https://ftp.yzu.edu.tw/CRAN/src/contrib/mgcv_1.8-19.tar.gz'

Content type 'application/octet-stream' length 868165 bytes (847 KB)

==================================================

downloaded 847 KB


trying URL 'https://ftp.yzu.edu.tw/CRAN/src/contrib/RcppArmadillo_0.7.960.1.2.tar.gz'

Content type 'application/octet-stream' length 1116748 bytes (1.1 MB)

==================================================

downloaded 1.1 MB


* installing *source* package ‘mgcv’ ...

** package ‘mgcv’ successfully unpacked and MD5 sums checked

** libs

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c coxph.c -o coxph.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c discrete.c -o discrete.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c gdi.c -o gdi.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c magic.c -o magic.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c mat.c -o mat.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrix.c -o matrix.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c mgcv.c -o mgcv.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c misc.c -o misc.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c mvn.c -o mvn.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c qp.c -o qp.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c soap.c -o soap.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sparse-smooth.c -o sparse-smooth.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c tprs.c -o tprs.o

clang -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 mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'

ld: library not found for -lgfortran

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [mgcv.so] Error 1

ERROR: compilation failed for package ‘mgcv’

* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’

* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’

* installing *source* package ‘RcppArmadillo’ ...

** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether clang++ accepts -g... yes

checking how to run the C++ preprocessor... clang++ -E

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether clang++ accepts -g... (cached) yes

checking whether g++ version is sufficient... checking LAPACK_LIBS... fallback LAPACK from R 3.3.0 or later used

checking for macOS... found

configure: WARNING: OpenMP unavailable and turned off.

configure: creating ./config.status

config.status: creating inst/include/RcppArmadilloConfigGenerated.h

config.status: creating src/Makevars

** libs

clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -I../inst/include  -fPIC  -Wall -mtune=core2 -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o

clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -I../inst/include  -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o

clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -I../inst/include  -fPIC  -Wall -mtune=core2 -g -O2 -c fastLm.cpp -o fastLm.o

clang++ -std=c++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 RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'

ld: library not found for -lgfortran

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [RcppArmadillo.so] Error 1

ERROR: compilation failed for package ‘RcppArmadillo’

* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo’

* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo’


The downloaded source packages are in

‘/private/var/folders/rm/tqs8q04d7dg59crpg05pfd1w0000gn/T/Rtmpy19PRb/downloaded_packages’

Warning messages:

1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  installation of package ‘mgcv’ had non-zero exit status

2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  installation of package ‘RcppArmadillo’ had non-zero exit status
diffbind • 1.9k views
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2
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 4 weeks ago
Cambridge, UK

Setting bDB=TRUE and bNotDB=TRUE makes dba.report() operate in an entirely different mode, and as a result will ignore the file= parameter. In this mode, instead of returning a report (GRanges object), it makes a new DBA object consisting of the sets of peaks you requested. This can then be used to make venn diagrams etc.

If you want to see all the sites in a report saved to disk, you can set the threshold to 1 (th=1), which will include all sites:

> h3k27ac.DB <- dba.report(h3k27ac, contrast = 1, method = DBA_EDGER_BLOCK, 
                           th = 1, bUsePval = FALSE, bNormalized = TRUE, 
                           bCalled = TRUE, bCounts = TRUE, bCalledDetail = TRUE, 
                           file = "H3K27ac_Sex_BlockFeatherType_FDR.05")

-Rory
ADD COMMENT •
0
Entering edit mode

Thanks a lot

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1
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 4 weeks ago
Cambridge, UK

Bioconductor 3.5 (which includes DiffBind 2.4) requires R 3.4. So you need to install R 3.4, when when you run biocLite it will update everything to current versions. dba.plotVolcano() was introduced in the current release so you won't see it until you update.

For dba.report(), you need to set bDB=TRUE for the other parameters to work (and get back a DBA object instead of a report).

-Rory
ADD COMMENT •
0
Entering edit mode

Many thanks

ADD REPLY •
0
Entering edit mode

I have installed R 3.4. However, when I run dba.report() with bDB = TRUE, and bNotDB = TRUE, I can see the corresponding values in Global Environment, but there is still no the corresponding file in my working directory (the detail below). Could you help me more? Many thanks.

h3k27ac.DB <- dba.report(h3k27ac, contrast = 1, method = DBA_EDGER_BLOCK, th = .05, bUsePval = FALSE, bNormalized = TRUE, bCalled = TRUE, bCounts = TRUE, bCalledDetail = TRUE, bDB = TRUE, bNotDB = TRUE, file = "H3K27ac_Sex_BlockFeatherType_FDR.05")

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