Description Usage Arguments Value Methods (by class) Note Examples
These methods lets you query and change the naming of genes in your pangenome. Take note that even though sequences are not in memory for pgLM objects, the names are. This means that changes to the description header in the underlying fasta files have no effect on the naming in your pangenome
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | geneNames(object)
geneNames(object) <- value
## S4 method for signature 'pgLM'
geneNames(object)
## S4 replacement method for signature 'pgLM'
geneNames(object) <- value
## S4 method for signature 'pgFull'
geneNames(object)
## S4 replacement method for signature 'pgFull'
geneNames(object) <- value
## S4 method for signature 'pgSlim'
geneNames(object)
## S4 replacement method for signature 'pgSlim'
geneNames(object) <- value
|
object |
A pgVirtual subclass |
value |
A character vector with new names |
In case of the getter, a character vector containing the names of each gene.
pgLM
: Get genenames for pgLM and subclasses
pgLM
: Set genenames for pgLM and subclasses
pgFull
: Get genenames for pgFull and subclasses
pgFull
: Set genenames for pgFull and subclasses
pgSlim
: Throws error for pgSlim
pgSlim
: Throws error for pgSlim
Required for subclasses of pgVirtual in order to extend the class system of FindMyFriends
1 2 3 4 | testPG <- .loadPgExample()
head(geneNames(testPG))
geneNames(testPG)[10] <- 'Gene number 10'
|
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