PhIPData-methods {PhIPData} | R Documentation |
Methods to extract and modify assay(s)
(including
convenient functions for counts
, logfc
, and prob
),
sampleInfo
, peptideInfo
, and metadata
.
## S4 method for signature 'PhIPData' counts(object, ...) logfc(object, ...) ## S4 method for signature 'PhIPData' logfc(object, ...) prob(object, ...) ## S4 method for signature 'PhIPData' prob(object, ...) peptideInfo(object, ...) ## S4 method for signature 'PhIPData' peptideInfo(object, ...) sampleInfo(object, ...) ## S4 method for signature 'PhIPData' sampleInfo(object, ...) ## S4 replacement method for signature 'PhIPData,list' assays(x, withDimnames = TRUE, ...) <- value ## S4 replacement method for signature 'PhIPData,SimpleList' assays(x, withDimnames = TRUE, ...) <- value ## S4 replacement method for signature 'PhIPData,missing' assay(x, i, withDimnames = TRUE, ...) <- value ## S4 replacement method for signature 'PhIPData,numeric' assay(x, i, withDimnames = TRUE, ...) <- value ## S4 replacement method for signature 'PhIPData,character' assay(x, i, withDimnames = TRUE, ...) <- value ## S4 replacement method for signature 'PhIPData' counts(object, ...) <- value logfc(object, ...) <- value ## S4 replacement method for signature 'PhIPData' logfc(object, ...) <- value prob(object, ...) <- value ## S4 replacement method for signature 'PhIPData' prob(object, ...) <- value peptideInfo(object) <- value ## S4 replacement method for signature 'PhIPData' peptideInfo(object) <- value sampleInfo(object, ...) <- value ## S4 replacement method for signature 'PhIPData' sampleInfo(object) <- value
object |
A |
... |
parameters for |
x |
A |
withDimnames |
Parameter for RangedSummarizedExperiment class functions. Overrided since row/column names are automatically synced within each object. |
value |
A |
i |
A |
In addition to the functions detailed in
RangedSummarizedExperiment, the PhIPData
class includes
conveniently named functions to quickly access and modify frequently used
components of PhIPData objects.
Replacement functions ensure that names of the replacement object are matched
with the names of the PhIPData
object.
Since packages for identifying differential expression in RNA-seq experiments are frequently used for estimating fold-changes for peptide enrichments, the class also includes coercion methods to and from DGELists.
Accessors: a DataFrame object
Setters: a PhIPData
object
In the following code snippets, x
is a PhIPData object,
value
is a matrix-like object with the same dimensions as x
,
and ...
are further arguments passed to assay
(for the getter) or assay<-
(for the setter).
counts(x, ...)
, counts(x, ...) <- value
:Get or set a matrix of raw read counts
logfc(x, ...)
, logfc(x, ...) <- value
:Get or set a matrix of log2 estimated fold changes (in comparison to beads-only samples)
prob(x, ...)
, pob(x, ...) <- value
:Get or set a matrix of probabilities associated with whether a sample has an enriched antibody response for a peptide.
assays
for
SummarizedExperiment operations.
example("PhIPData") replacement_dat <- matrix(1L, nrow = 5, ncol = 5) ## SummarizedExperiment Accessors and Setters assays(phip_obj) assays(phip_obj)$counts <- replacement_dat assay(phip_obj, "logfc") assay(phip_obj, "logfc") <- replacement_dat ## counts counts(phip_obj) counts(phip_obj) <- counts_dat ## logfc logfc(phip_obj) logfc(phip_obj) <- logfc_dat ## prob prob(phip_obj) prob(phip_obj) <- replacement_dat ## coercion functions as(phip_obj, "DGEList") as(phip_obj, "List") as(phip_obj, "list")