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" <karolis.uzi...@scilifelab.se>
Date: Feb 19, 2015 9:22 AM
Subject: readGAlignmentsFromBam function
To: "Michael Lawrence" <lawrence.mich...@gene.com>
Cc: "bioconduc...@r-project.org" <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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