ScpModel-class: Class to store the results of single-cell proteomics...

In UCLouvain-CBIO/scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Class to store the results of single-cell proteomics modelling

Description

An ScpModel object must be always stored in the metadata() of an object that inherits from the SingleCellExperiment class. The ScpModel object should never be accessed directly by the user. Instead, we provide several setter function to retrieve information that may be useful to the user.The ScpModel class contains several slots:

• scpModelFormula: a formula object controlling which variables are to be modelled.

• scpModelInputIndex: a numeric(1), selecting the assay to use in the SingleCellExperiment object as input matrix. Note that this slot serves as a pointer, meaning that the quantitative data is not duplicated. Any change to the assay in the SingleCellExperiment will impact the estimation of the ScpModel object.

• scpModelFilterThreshold: A numeric(1) indicating the minimal n/p ratio required for a feature to be included in further model exploration. n/p is the number of measured values for a features divided by the number of coefficients to estimate. n/p cannot be smaller than 1 because this would lead to over-specified models.

• scpModelFitList: A List that contains the model results for each feature. Each element is a ScpModelFit object (see ScpModelFit)

Usage

scpModelFormula(object, name)

scpModelInput(object, name, filtered = TRUE)

scpModelFilterThreshold(object, name)

scpModelFilterNPRatio(object, name, filtered = TRUE)

scpModelResiduals(object, name, join = TRUE, filtered = TRUE)

scpModelEffects(object, name, join = TRUE, filtered = TRUE)

scpModelNames(object)

scpModelFilterThreshold(object, name) <- value

Arguments

object	An object that inherits from the SingleCellExperiment class.
name	A character(1) providing the name to use to store or retrieve the modelling results. When retrieving a model and name is missing, the name of the first model found in object is used.
filtered	A logical(1) indicating whether the output should return all features (FALSE) or the features that comply to the n/p ratio threshold (TRUE).
join	A logical(1) indicating whether the output should be combined in a single matrix (TRUE) or it should be returned as a list with one element for each feature (FALSE). When TRUE, any gaps across features will be filled with NA's.
value	An numeric(1), the new value for the n/p ratio threshold

Getters

Each slot has a getter function associated:

• scpModelNames(): returns a vector of names of ScpModel objects stored in the SingleCellExperiment object.

• scpModelFormula(): returns the formula slot of the ScpModel within an object that inherits from the SummarizedExperiment class.

• scpModelFilterThreshold(): returns the n/p ration threshold used for feature filtering.

• scpModelInput(): returns a matrix with the quantitative values used as input of the model. Hence, the matrix contains the data before modelling. If filtered = TRUE, the feature of the matrix are restricted to the features that satisfy the n/p ratio threshold.

• scpModelFilterNPRatio(): returns the computed n/p ratio for each feature. If filtered = TRUE, the function returns only the n/p of the features that satisfy the n/p ratio threshold.

• scpModelResiduals(): when join = FALSE, the function returns a list where each element corresponds to a feature and contains the estimated residuals. When join = TRUE (default), the function combines the list into a matrix with features in rows and cells in columns, and filling the gaps with NA. If filtered = TRUE, the feature of the matrix are restricted to the features that satisfy the n/p ratio threshold.

• scpModelEffects(): when join = FALSE, the function return a list where each element of the list corresponds to a feature. Each element contains another list with as many elements as variable in the model and each element contains the data effect vector for that vector. When join = TRUE (default), each element of the list is a matrix with features in rows and cells in columns where gaps are filled with NA. If filtered = TRUE, the feature of the matrix are restricted to the features that satisfy the n/p ratio threshold.

Setter:

• ⁠scpModelFilterThreshold<-()⁠: the function changes the n/p ratio threshold used for filtering features.

Author(s)

Christophe Vanderaa, Laurent Gatto

See Also

• ScpModelFit for a description of the class that store modelling results

• ScpModel-Workflow that uses the class to store the estimated model.

Examples

data("leduc_minimal")

####---- Getters ----####

scpModelNames(leduc_minimal)

scpModelFormula(leduc_minimal)

dim(leduc_minimal)
dim(scpModelInput(leduc_minimal))
dim(scpModelInput(leduc_minimal, filtered = FALSE))

head(scpModelFilterNPRatio(leduc_minimal))

dim(scpModelResiduals(leduc_minimal))
dim(scpModelResiduals(leduc_minimal, filtered = FALSE))
scpModelResiduals(leduc_minimal, join = FALSE)

scpModelEffects(leduc_minimal)
dim(scpModelEffects(leduc_minimal)$Set)
dim(scpModelEffects(leduc_minimal, filtered = FALSE)$Set)
scpModelEffects(leduc_minimal, join = FALSE)[[1]]

scpModelFilterThreshold(leduc_minimal)

####---- Setter ----####

scpModelFilterThreshold(leduc_minimal) <- 2
scpModelFilterThreshold(leduc_minimal)

UCLouvain-CBIO/scp documentation built on Oct. 12, 2024, 2:37 a.m.