create_annotation | R Documentation |
This function generates transcript basic annotation data tables starting from GTF files or TxDb objects. Annotation data tables include a column named transcript reporting the name of the reference transcripts and four columns named l_tr, l_utr5, l_cds and l_utr3 reporting the length of the transcripts and of their annotated 5' UTRs, CDSs and 3' UTRs, respectively. Please note: if a transcript region is not annotated its length is set to 0.
create_annotation(gtfpath = NULL, txdb = NULL, dataSource = NA, organism = NA)
gtfpath |
A character string specifying the path to a GTF file,
including its name and extension. Please make sure the GTF file derives
from the same release of the sequences used in the alignment step. Note
that either |
txdb |
Character string specifying the TxDb annotation package to be
loaded. If not already present in the system, it is automatically installed
through the biocLite.R script (check
here
the list of available TxDb annotation packages). Please make sure the TxDb
annotation package derives from the same release of the sequences used in
the alignment step. Note that either |
dataSource |
Optional character string describing the origin of the GTF
data file. This parameter is considered only if |
organism |
Optional character string reporting the genus and species of
the organism of the GTF data file. This parameter is considered only if
|
A data table.
## gtf_file <- "path/to/GTF/file.GTF"
## create_annotation(gtfpath = gtf_file, dataSource = "gencode6", organism = "Mus musculus")
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