makeTxDb: Making a TxDb object from user supplied annotations

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/makeTxDb.R

Description

makeTxDb is a low-level constructor for making a TxDb object from user supplied transcript annotations.

Note that the end user will rarely need to use makeTxDb directly but will typically use one of the high-level constructors makeTxDbFromUCSC, makeTxDbFromEnsembl, or makeTxDbFromGFF.

Usage

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makeTxDb(transcripts, splicings, genes=NULL,
         chrominfo=NULL, metadata=NULL,
         reassign.ids=FALSE, on.foreign.transcripts=c("error", "drop"))

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 organism, genome, UCSC table, etc... The names of the columns must be "name" and "value" and their type must be character.

reassign.ids

TRUE or FALSE. 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 (the default) 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.

on.foreign.transcripts

Controls what to do when the input contains foreign transcripts i.e. transcripts that are on sequences not in chrominfo. If set to "error" (the default)

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 should not be supplied if transcripts has a gene_id column. If supplied, it 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 TxDb object.

Author(s)

Hervé Pagès

See Also

Examples

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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),
                   cds_phase=c(0, 0, 2, 0, NA, NA))

txdb <- makeTxDb(transcripts, splicings)

Bioconductor/GenomicFeatures documentation built on May 25, 2021, 5:47 a.m.