Re: [Bioc-devel] enable windows build for eiR

[Obenchain, Valerie]

Done. I also bumped the version. We missed the cutoff for today so we
should see the Windows build on the March 16 report.

Valerie


On 03/14/2017 03:09 PM, kho...@cs.ucr.edu wrote:
> Can you please enable building on windows again for package eiR in
> development (current version is 1.15.3)? Not for current release though.
> Thanks.
>
> Kevin
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] MSA Consensus

[Ulrich Bodenhofer]

Hi Natalie,

Sorry, there is presently no such function in the 'msa' package and, as 
far as I know, there is no such thing in 'Biostrings' either. If you can 
specify us an exact formula how to compute the score you are 
particularly interested in (or at least point us to a reference), we can 
try to implement it before the next major release in April. Note that 
the msaPrettyPrint() function is just a wrapper around the LaTeX package 
'texshade'. No matter what 'texshade' may do internally, we have no 
access to its internal functionality from R.


Thanks and best regards,
Ulrich


Date: Mon, 13 Mar 2017 17:36:22 +
From: Natalie Stephenson 
To: "bioc-devel@r-project.org" 
Subject: [Bioc-devel] MSA Consensus
Message-ID:



Content-Type: text/plain; charset="UTF-8"

Hi,

I was wondering if you would be able to tell me whether it is possible to get 
the calculated conservation score (GONNET PAM250 matrix) from an alignment 
produced by MSA?
>From what I understand from your literature, this is something that is 
calculated in msa by ClustalW, as it is possible to specify an arbitrary (. : !) 
identifier based on this score when performing msaPrettyPrint(). However, I would 
prefer to specify an output that gave consensus sequence with a numeric PAM 
conservation score for each residue position in the alignment. Is this something 
that I can get from the msa tool?

Thanks for your advice of this matter.

Best wishes,
Natalie


___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Chromosome order in GRangesForUCSCGenome

[Bernat Gel]

Great, thanks

*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
b...@igtp.cat 
www.germanstrias.org 









El 03/13/2017 a las 01:57 PM, Michael Lawrence escribió:
Looks like UCSC has started sorting the chromosomes by size.  I made 
1.35.9 use sortSeqlevels() to normalize the order of them.


On Mon, Mar 13, 2017 at 3:05 AM, Bernat Gel > wrote:


I'm downloading genome information from UCSC using the
GRangesForUCSCGenome from rtracklayer and it seems that the
chromosome order is incorrect (or at least non-canonical).

> seqlevels(GRangesForUCSCGenome(genome="hg19"))

[1] "chr1"  "chr2" "chr3" "chr4" "chr5"
[6] "chr6"  "chr7" "chrX" "chr8" "chr9"
[11] "chr10" "chr11" "chr12"  "chr13" "chr14"
[16] "chr15" "chr16" "chr17"  "chr18" "chr20"
[21] "chrY"  "chr19" "chr22"  "chr21" "chr6_ssto_hap7"
[26] ...

With chrX before chr8  and Y before chr19.

And the same happens with SeqinfoForUCSCGenome(genome="hg19")

I know I could reorder them manually, but I'm downloading this
from various genomes to cache them in a package (karyoploteR) and
I'd rather not rely on manual sorting for that.

I'm quite sure it used to return them in the canonical order. Is
there anything I'm missing or is it a bug somewhere?


Thanks a lot

Bernat




sessionInfo()
R Under development (unstable) (2016-11-07 r71637)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C
 LC_COLLATE=en_US.utf8 LC_MONETARY=en_US.utf8
 [6] LC_MESSAGES=en_US.utf8LC_PAPER=es_ES.UTF-8 LC_NAME=C 
   LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils
datasets  methods   base

other attached packages:
 [1] testthat_1.0.2karyoploteR_0.99.8 biovizBase_1.23.2   
 regioneR_1.7.1BSgenome_1.43.2 rtracklayer_1.35.1

 [7] Biostrings_2.43.2 XVector_0.15.0 GenomicRanges_1.27.18
GenomeInfoDb_1.11.6   IRanges_2.9.14 S4Vectors_0.13.5
[13] BiocGenerics_0.21.1   memoise_1.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8   lattice_0.20-34
Rsamtools_1.27.11 assertthat_0.1
 [5] digest_0.6.11 mime_0.5 R6_2.2.0  
plyr_1.8.4
 [9] backports_1.0.4   acepack_1.4.1 RSQLite_1.1-2   
 httr_1.2.1

[13] ggplot2_2.2.1 BiocInstaller_1.25.3
zlibbioc_1.21.0   GenomicFeatures_1.27.6
[17] lazyeval_0.2.0data.table_1.10.0 rpart_4.1-10 
Matrix_1.2-7.1

[21] checkmate_1.8.2   splines_3.4.0
BiocParallel_1.9.4AnnotationHub_2.7.9
[25] stringr_1.1.0 foreign_0.8-67
ProtGenerics_1.7.0RCurl_1.95-4.8
[29] biomaRt_2.31.3munsell_0.4.3 shiny_0.14.2 
httpuv_1.3.3
[33] base64enc_0.1-3   htmltools_0.3.5 nnet_7.3-12   
   SummarizedExperiment_1.5.3
[37] tibble_1.2gridExtra_2.2.1 htmlTable_1.8 
   interactiveDisplayBase_1.13.0
[41] Hmisc_4.0-2   XML_3.98-1.5 crayon_1.3.2 
GenomicAlignments_1.11.6
[45] bitops_1.0-6  grid_3.4.0 xtable_1.8-2
gtable_0.2.0
[49] DBI_0.5-1 magrittr_1.5 scales_0.4.1 
stringi_1.1.2

[53] latticeExtra_0.6-28   Formula_1.2-1
RColorBrewer_1.1-2ensembldb_1.99.10
[57] tools_3.4.0   dichromat_2.0-0 Biobase_2.35.0 
  survival_2.40-1

[61] yaml_2.1.14   AnnotationDbi_1.37.0
colorspace_1.3-2  cluster_2.0.5
[65] VariantAnnotation_1.21.14 knitr_1.15.1


-- 


*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068 
Fax: (+34) 93 497 8654 
08916 Badalona, 

[Bioc-devel] MSA Consensus

[Natalie Stephenson]

Hi,

I was wondering if you would be able to tell me whether it is possible to get 
the calculated conservation score (GONNET PAM250 matrix) from an alignment 
produced by MSA?
>From what I understand from your literature, this is something that is 
>calculated in msa by ClustalW, as it is possible to specify an arbitrary (. : 
>!) identifier based on this score when performing msaPrettyPrint(). However, I 
>would prefer to specify an output that gave consensus sequence with a numeric 
>PAM conservation score for each residue position in the alignment. Is this 
>something that I can get from the msa tool?

Thanks for your advice of this matter.

Best wishes,
Natalie

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] GRangesList Conversion Fails For Unstranded Sequencing Data

[Dario Strbenac]

Good day,

countOverlaps doesn't work for a GAlignmentPairs object with strandMode set to 
0. This is because of an oversight in the grglist function. It has an if 
statement that checks whether the strand mode is 1 or 2. Then, it tries to 
subset the variable 'x_unlisted'. However, if strand mode is 0, neither of the 
conditional sections of code are executed and Error in .local(x, use.names, 
use.mcols, ...) : object 'x_unlisted' not found happens because the 
'x_unlisted' variable has not been created. It's a surprise no one else has 
encountered this bug before.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel