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GenomicFeatures (version 1.18.7)

extractTranscriptsFromGenome: Various DEFUNCT tools for extracting transcript sequences

Description

WARNING: Starting with BioC 3.0, the tools described in this man page are DEFUNCT.

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

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

Related utility:

sortExonsByRank orders (or reorders) by rank the exons stored in a GRangesList object containing exons grouped by transcript. DEPRECATED. No replacement.

Usage

# DEFUNCT. Please use extractTranscriptSeqs() instead.
extractTranscriptsFromGenome(genome, txdb, decreasing.rank.on.minus.strand=FALSE, use.names=TRUE)


# DEFUNCT. Please use extractTranscriptSeqs() instead.
extractTranscripts(x, exonStarts=list(), exonEnds=list(), strand=character(0), decreasing.rank.on.minus.strand=FALSE)


# DEPRECATED. No replacement.
sortExonsByRank(x, decreasing.rank.on.minus.strand=FALSE)

Arguments

genome
A BSgenome object. See the available.genomes function in the BSgenome package for how to install a genome.
txdb
A TxDb object or a GRangesList object.
decreasing.rank.on.minus.strand
TRUE or FALSE. Describes the order of exons in transcripts located on the minus strand: are they ordered by increasing (default) or decreasing rank? For all the functions described in this man page (except sortExonsByRank), this argument describes the input. For sortExonsByRank, it describes how exons should be ordered in the output.
use.names
TRUE or FALSE. Ignored if txdb is not a TxDb object. If TRUE (the default), the returned sequences are named with the transcript names. If FALSE, they are named with the transcript internal ids. Note that, unlike the transcript internal ids, the transcript names are not guaranteed to be unique or even defined (they could be all NAs). A warning is issued when this happens.
x
A DNAString or MaskedDNAString object for extractTranscripts.

A GRangesList object for sortExonsByRank, typically coming from exonsBy(... , by="tx").

exonStarts, exonEnds
The starts and ends of the exons, respectively.

Each argument can be a list of integer vectors, an IntegerList object, or a character vector where each element is a comma-separated list of integers. In addition, the lists represented by exonStarts and exonEnds must have the same shape i.e. have the same lengths and have elements of the same lengths. The length of exonStarts and exonEnds is the number of transcripts.

strand
A character vector of the same length as exonStarts and exonEnds specifying the strand ("+" or "-") from which the transcript is coming.

Value

For extractTranscriptsFromGenome: A named DNAStringSet object with one element per transcript. When txdb is a GRangesList object, elements in the output align with elements in the input (txdb), and they have the same names.For extractTranscripts: A DNAStringSet object with one element per transcript.For sortExonsByRank: A GRangesList object with one top-level element per transcript. More precisely, the returned object has the same "shape" (i.e. same length and same number of elements per top-level element) as the input GRangesList object x.

See Also

extractTranscriptSeqs as a replacement for extractTranscriptsFromGenome and extractTranscripts.