[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.

---------- Forwarded message ----------
From: "Karolis Uziela" <karolis.uziela at scilifelab.se>
Date: Feb 19, 2015 9:22 AM
Subject: readGAlignmentsFromBam function
To: "Michael Lawrence" <lawrence.michael at gene.com>
Cc: "bioconductor at r-project.org" <bioconductor at 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

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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