GeneSpec | R Documentation |
A GeneSpec
consists of the gene IDs (possibly named with labels),
the summary function and the name of the summary function.
new()
Creates a new GeneSpec
object.
GeneSpec$new(genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))
genes
(named character
or NULL
)
the gene IDs, where the names
are used as labels if available.
fun
(function
or NULL
)
summary function. If NULL
is
used then multiple genes are not summarized but returned as a matrix from the
extract
method.
fun_name
(string
)
name of the summary function.
A new GeneSpec
object.
get_genes()
Returns the genes.
GeneSpec$get_genes()
get_gene_labels()
Returns the gene labels (substituted by gene IDs if not available).
GeneSpec$get_gene_labels(genes = self$get_genes())
genes
(character
)
for which subset of genes the labels should be returned.
returns_vector()
Predicate whether the extract returns a vector or not.
GeneSpec$returns_vector()
get_label()
Returns a string which can be used e.g. for plot labels.
GeneSpec$get_label(genes = self$get_genes())
genes
(character
)
for which subset of genes the labels should be returned.
extract()
Extract the gene values from an assay as specified.
GeneSpec$extract(assay)
assay
(matrix
)
original matrix with rownames containing the
specified genes.
Either a vector with one value per column, or a matrix with multiple genes in the rows.
extract_data_frame()
Extract the gene values as a data.frame
.
GeneSpec$extract_data_frame(assay)
assay
(matrix
)
original matrix with rownames containing the
specified genes.
A data.frame
with the genes in the columns and the samples
in the rows.
clone()
The objects of this class are cloneable with this method.
GeneSpec$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Minimal specification if only one gene is used. x_spec <- gene_spec("GeneID:1820") # Using multiple genes with a signature. x_spec <- gene_spec(c("GeneID:1820", "GeneID:52"), fun = colMeans) x_spec <- gene_spec(c("GeneID:1820", "GeneID:52"), fun = colPrinComp1) x_spec$returns_vector() x_spec$get_genes() x_spec$get_gene_labels() x_spec$get_label() # Using multiple genes with partial labels, without a signature. x_spec <- gene_spec(c(A = "GeneID:1820", "GeneID:52")) x_spec$returns_vector() x_spec$get_gene_labels() # Use the gene specification to extract genes from a matrix. mat <- matrix( data = rpois(15, 10), nrow = 3, ncol = 5, dimnames = list(c("GeneID:1820", "GeneID:52", "GeneID:523"), NULL) ) x_spec$extract(mat) # We can also extract these as a `data.frame`. x_spec$extract_data_frame(mat)
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