makeTranscriptDb {GenomicFeatures}R Documentation

Making a TranscriptDb object from user supplied annotations

Description

makeTranscriptDb is a low-level constructor for making a TranscriptDb object from user supplied transcript annotations. See ?makeTranscriptDbFromUCSC and ?makeTranscriptDbFromBiomart for higher-level functions that feed data from the UCSC or BioMart sources to makeTranscriptDb.

Usage

  makeTranscriptDb(transcripts, splicings,
                   genes=NULL, chrominfo=NULL, metadata=NULL,
                   reassign.ids=FALSE)

Arguments

transcripts

data frame containing the genomic locations of a set of transcripts

splicings

data frame containing the exon and cds locations of a set of transcripts

genes

data frame containing the genes associated to a set of transcripts

chrominfo

data frame containing information about the chromosomes hosting the set of transcripts

metadata

2-column data frame containing meta information about this set of transcripts like species, organism, genome, UCSC table, etc... The names of the columns must be "name" and "value" and their type must be character.

reassign.ids

controls how internal ids should be assigned for each type of feature i.e. for transcripts, exons, and cds. For each type, if reassign.ids is FALSE and if the ids are supplied, then they are used as the internal ids, otherwise the internal ids are assigned in a way that is compatible with the order defined by ordering the features first by chromosome, then by strand, then by start, and finally by end.

Details

The transcripts (required), splicings (required) and genes (optional) arguments must be data frames that describe a set of transcripts and the genomic features related to them (exons, cds and genes at the moment). The chrominfo (optional) argument must be a data frame containing chromosome information like the length of each chromosome.

transcripts must have 1 row per transcript and the following columns:

Other columns, if any, are ignored (with a warning).

splicings must have N rows per transcript, where N is the nb of exons in the transcript. Each row describes an exon plus, optionally, the cds contained in this exon. Its columns must be:

Other columns, if any, are ignored (with a warning).

genes must have N rows per transcript, where N is the nb of genes linked to the transcript (N will be 1 most of the time). Its columns must be:

Other columns, if any, are ignored (with a warning).

chrominfo must have 1 row per chromosome and the following columns:

Other columns, if any, are ignored (with a warning).

Value

A TranscriptDb object.

Author(s)

H. Pages

See Also

Examples

transcripts <- data.frame(
                   tx_id=1:3,
                   tx_chrom="chr1",
                   tx_strand=c("-", "+", "+"),
                   tx_start=c(1, 2001, 2001),
                   tx_end=c(999, 2199, 2199))
splicings <-  data.frame(
                   tx_id=c(1L, 2L, 2L, 2L, 3L, 3L),
                   exon_rank=c(1, 1, 2, 3, 1, 2),
                   exon_start=c(1, 2001, 2101, 2131, 2001, 2131),
                   exon_end=c(999, 2085, 2144, 2199, 2085, 2199),
                   cds_start=c(1, 2022, 2101, 2131, NA, NA),
                   cds_end=c(999, 2085, 2144, 2193, NA, NA))

txdb <- makeTranscriptDb(transcripts, splicings)

[Package GenomicFeatures version 1.14.2 Index]