[Bioc-devel] deprecated extractTranscriptsFromGenome

Hi Raf,

Under ?extractTranscriptsFromGenome I see this:

Description:

WARNING: The tools described in this man page are obsolete and in
the process of being DEPRECATED.

?extractTranscriptsFromGenome? extracts the transcript sequences
from a BSgenome data package using the transcript information
(exon boundaries) stored in a TranscriptDb or GRangesList object.
DEPRECATED. Please use ?extractTranscriptSeqs? instead.

?extractTranscripts? extracts a set of transcripts from a single
DNA sequence. DEPRECATED. Please use ?extractTranscriptSeqs?
instead.

Related utilities:

?transcriptWidths? to get the lengths of the transcripts (called
the "widths" in this context) based on the boundaries of their
exons.

?transcriptLocs2refLocs? converts transcript-based locations into
reference-based (aka chromosome-based or genomic) locations.

?sortExonsByRank? orders (or reorders) by rank the exons stored in
a GRangesList object containing exons grouped by transcript.


Best,

Jim

Hi, I am the maintainer of chimera package
I got an warning indicating the extractTranscriptsFromGenome and
extractTranscripts functions from GenomicFeatures package are deprecated.
Does anybody could tell me which are the functions that are going to
substitute them?
Cheers
Raf

James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099