Description Usage Arguments Details Value Author(s) Examples
The function searches in the given data for unique gene_id
values.
For each item, values like gene_id, seqid and strand are extracted.
Optionally (when present) also gene_name and gene_biotype are extracted.
The function assignes unique id values which are ordered by gene_id values
(not genetic positions). Owing to this, id values equal
as.numeric(gene_id)
.
1 | getGenePositions(object,by,force=FALSE,...)
|
object |
ensemblGenome, ucscGenome or ensemblJunctions. Object from which gene positions are extracted. |
by |
Character. Determines criterion by which genes are discerned. Accepted values: "gene_id" and "gene_name". For Ensembl genomes the default is 'gene_id' and for USCC genomes the default is 'gene_name'. |
force |
Logical. When FALSE, gene positions will only be calculated when a position table is not present in local environment. The function then returns a copy. |
... |
Unused. |
The function stores a copy of the result in the internal environment
(genes
table). Upon subsequent calls the values only are re-calculated
when force=TRUE is given. Otherwise the function returns a copy of the
contained table.
Present genes
tables will be automatically saved and restored by
saveGenome
and load.X
functions.
data.frame
Wolfgang Kaisers
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ##-------------------------------------##
## A) Ensembl genome:
##-------------------------------------##
ensfile <- system.file("extdata",
"hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)
gp <- getGenePositions(ens)
##-------------------------------------##
## B) Ensembl junctions:
##-------------------------------------##
junc <- getSpliceTable(ens)
genes <- getGenePositions(junc)
##-------------------------------------##
# C) Ucsc genome:
##-------------------------------------##
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
junc <- getSpliceTable(uc)
gp <- getGenePositions(junc)
|
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