compareTranscripts: compare alternatively-spliced transcripts

In GoekeLab/bambu: Context-Aware Transcript Quantification from Long Read RNA-Seq data

compare alternatively-spliced transcripts

Description

compare alternatively-spliced transcripts

Usage

compareTranscripts(query, subject)

Arguments

query	a GRangesList of transcripts
subject	a GRangesList of transcripts

Details

This function compares two alternatively-spliced transcripts and returns a tibble object that determines the type of the alternative splicing between the query and the subject transcript. Alternative splicing includes exons skipping, intron retention, alternative 5' exon start site, alternative 3' exon end site, alternative first exon, alternative last exon, alternative transcription start site (TSS), alternative transcription end site (TES), internal first exon, internal last exon, or a mixed combination of them.

Value

a tibble object with the following columns:

Remark: two exons, one each from query and subject transcript are defined to be equivalent if one of the exons fully covers the another exon.

• alternativeFirstExon: FALSE if query transcript and subject transcript have equivalent first exon. TRUE otherwise.

• alternativeTSS: +k if the query initiates the transcription k sites earlier than the subject transcript, -k if the query initiates the transcription k sites later than the subject transcript.

• internalFirstExon.query: TRUE if the first exon of the query transcript is equivalent to one of the exon of the subject transcript (except the first exon). FALSE otherwise.

• internalFirstExon.subject: TRUE if the first exon of the subject transcript is equivalent to one of the exon of the query transcript (except the first exon). FALSE otherwise.

• alternativeLastExon: FALSE if query transcript and subject transcript have equivalent last exon. TRUE otherwise.

• alternativeTES: +k if the query transcript ends the transcription k sites later than the subject transcript, -k if the query transcript ends the transcription k sites earlier than the subject transcript.

• internalLastExon.query: TRUE if the last exon of the query transcript is equivalent to one of the exon in the subject transcript (except the last exon). FALSE otherwise.

• internalLastExon.subject: TRUE if the last exon of the subject transcript is equivalent to one of the exon in the query transcript (except the last exon). FALSE otherwise.

• intronRetention.subject: k if there is/are k intron(s) in the subject transcript relative to the query transcript.

• intronRetention.query: k if there is/are k intron(s) in the query transcript relative to the subject transcript.

• exonSkipping.query: k if there is/are k exon(s) in the subject transcript (except the first and last) not in the query transcript.

• exonSkipping.subject: k if there is/are k exon(s) in the query transcript (except the first and last) not in the subject transcript.

• exon5prime (splicing): k if there is/are k equivalent exon(s) having different 5' start site (except the 5' start site of first exon).

• exon3prime (splicing): k if there is/are k equivalent exon(s) having different 3' end site (except the 3' end site of the last exon).

See Also

Value for more details about each of the alternative splicing events.

Examples

query <- readRDS(system.file("extdata", 
    "annotateSpliceOverlapByDist_testQuery.rds",
    package = "bambu"))
subject <- readRDS(system.file("extdata", 
    "annotateSpliceOverlapByDist_testSubject.rds",
    package = "bambu"))
compareTranscriptsTable <- compareTranscripts(query, subject)

compareTranscriptsTable

GoekeLab/bambu documentation built on Oct. 26, 2024, 9:45 a.m.