Re: [Bioc-devel] Fwd: readGAlignmentsFromBam function
Hi Karolis,
Please use the bioc-devel mailing list (to which you should
be subscribed) to ask this type of question.
If you manually run the example in your package (using BioC devel,
which requires R-3.2), you'll get:
> prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping)
Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf
[1] "Finished:
/home/hpages/R/R-3.2.r67773/library/prebsdata/sample_bam_files/input1.bam"
[1] "Finished:
/home/hpages/R/R-3.2.r67773/library/prebsdata/sample_bam_files/input2.bam"
Note: Some probe IDs contain duplicates.
Estimated values for Bayesian prior:
Alpha=1e-04
Beta=0.0136640101662362
Note: 41457 probe sequences are missing in _mapping.txt file.
Normalizing
Calculating Expression
Warning messages:
1: 'readGAlignmentsFromBam' is deprecated.
Use 'readGAlignments' instead.
See help("Deprecated")
2: 'readGAlignmentsFromBam' is deprecated.
Use 'readGAlignments' instead.
See help("Deprecated")
Hope this helps. Too bad 'R CMD check' truncates the deprecation
message :-/
Cheers,
H.
On 02/19/2015 01:15 PM, Michael Lawrence wrote:
-- Forwarded message --
From: "Karolis Uziela"
Date: Feb 19, 2015 9:22 AM
Subject: readGAlignmentsFromBam function
To: "Michael Lawrence"
Cc: "bioconduc...@r-project.org"
Hi,
I have looked at R check results for the devel version of Bioconductor and
I noticed that the package I developed ("prebs") gives this warning:
Warning: 'readGAlignmentsFromBam' is deprecated.
What is the new function that should be used instead of
readGAlignmentsFromBam (GenomicAlignments package)? Do the changes
affect readGAlignmentPairs function, too?
Regards,
Karolis
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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[Bioc-devel] Fwd: readGAlignmentsFromBam function
-- Forwarded message --
From: "Karolis Uziela"
Date: Feb 19, 2015 9:22 AM
Subject: readGAlignmentsFromBam function
To: "Michael Lawrence"
Cc: "bioconduc...@r-project.org"
Hi,
I have looked at R check results for the devel version of Bioconductor and
I noticed that the package I developed ("prebs") gives this warning:
Warning: 'readGAlignmentsFromBam' is deprecated.
What is the new function that should be used instead of
readGAlignmentsFromBam (GenomicAlignments package)? Do the changes
affect readGAlignmentPairs function, too?
Regards,
Karolis
--
Karolis Uziela
PhD student
Science for Life Laboratory
Box 1031
17121 Solna, Sweden
Mob. +46 729 120 395
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[Bioc-devel] GRanges to VRanges coercion
Hi Valerie, hi Michael,
I find myself frequently moving back and forth between data.frames, GRanges
and VRanges objects.
The makeGRangesFromDataFrame function from the GenomicRanges makes the
coercion between the former straightforward, but I couldn't find anything
similar for the second step, coercsion from GRanges to VRanges.
There is a coercion method defined in the GenomicRanges package:
getMethod(coerce, c("GRanges", "VRanges"))
Method Definition:
function (from, to = "VRanges", strict = TRUE)
{
obj <- new("VRanges")
as(obj, "GRanges") <- from
obj
}
Signatures:
from to
target "GRanges" "VRanges"
defined "GRanges" "VRanges"
but I haven't been able to get it to work (or find where it is documented).
The source code shown above doesn't indicate how the coercion method would
check for the presence of required / optional VRanges columns, e.g. 'ref',
'alt', 'altDepth', etc.
Would it be useful to add an explicit makeVRangesFromGRanges function to
the VariantAnnotation package ( and / or the corresponding coercion method)
?
Then it would be easy to go from a data.frame to a VRanges object, e.g. as
in this pseudocode:
makeVRangesFromGRanges(
makeGRangesFromDataFrame( data.frame )
)
You can find a first attempt at implementing the
makeVRangesFromGRanges function
here , which you are
welcome to use / modify if you find it useful.
If this functionality should already be available, I'd be happy to learn
about that, too !
Thank you,
Thomas
SessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] VariantAnnotation_1.12.9 Rsamtools_1.18.2 Biostrings_2.34.1
XVector_0.6.0GenomicRanges_1.18.4
[6] GenomeInfoDb_1.2.4 IRanges_2.0.1S4Vectors_0.4.0
BiocGenerics_0.12.1 BiocInstaller_1.16.1
[11] roxygen2_4.1.0 devtools_1.7.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.1base64enc_0.1-2 BatchJobs_1.5
BBmisc_1.9 Biobase_2.26.0
[6] BiocParallel_1.0.3 biomaRt_2.22.0 bitops_1.0-6
brew_1.0-6 BSgenome_1.34.1
[11] checkmate_1.5.1 codetools_0.2-10DBI_0.3.1
digest_0.6.8fail_1.2
[16] foreach_1.4.2 GenomicAlignments_1.2.1 GenomicFeatures_1.18.3
iterators_1.0.7 Rcpp_0.11.4
[21] RCurl_1.95-4.5 RSQLite_1.0.0 rtracklayer_1.26.2
sendmailR_1.2-1 stringr_0.6.2
[26] tools_3.1.2 XML_3.98-1.1zlibbioc_1.12.0
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Re: [Bioc-devel] GEOquery Warnings When Reading SOFT File
Hi Dario,
This isn't the right forum for your question (this listserv is for
development of packages, not questions about existing packages), so you
should ask on the support site.
Best,
Jim
On Thu, Feb 19, 2015 at 1:00 AM, Dario Strbenac
wrote:
> library(GEOquery)
> gastricChina <- getGEO("GSE65801", GSEMatrix = FALSE)
>
> Generates warnings
>
> > head(warnings(), 1)
> Warning message:
> In readLines(con, n = chunksize) :
> seek on a gzfile connection returned an internal error
>
> Does it affect the correctness of the imported data ?
>
> Also, experimentData(gastricChina) gives an empty result
>
> Experiment data
> Experimenter name:
> Laboratory:
> Contact information:
> Title:
> URL:
> PMIDs:
> No abstract available.
>
> whereas some of the fields are filled in on the webpage.
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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Re: [Bioc-devel] Documentation of GenomicRanges::follow etc. very hard to find
On 02/18/2015 07:50 PM, Hervé Pagès wrote:
I've not done this in a systematic way yet but this is the long
term plan. In the mean time, I just did it for the "precede", "follow",
"nearest", "distance", and "distanceToNearest" in GenomicRanges.
This is in GenomicRanges 1.19.38 (BioC devel). More will follow...
Many thanks. And I concur that it would be nice and useful to have a
more automatic kind of mechanism for this, but that seems a bigger
undertaking since it would involve changing R itself.
Cheers,
Philip
--
Philip Lijnzaad, PhD
Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 2.211
IM: plijnz...@jabber.org , philip.lijnz...@gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464
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