ResultObj: Function ResultObjClass

In CshlSiepelLab/ACE: Analysis of CRISPR Essentiality in R

Description

Function ResultObjClass

Function ResultObjClass

Details

An R6 object class to present the results of model fitting as produced by optimizeModelParameters. Not called by user, but rather within optimizeModelParameters.

Value

ResultObj R6 class object, with gene_essentiality, guide_efficiency, sample_response, guide_covariates, gene_essentiality_likelihood, gene_essentiality_CI, gene_essentiality_pvalue, differential_depletion_pvals, mean_var_model_parameters.

Public fields

gene_essentiality

Data.table of gene essentiality for all, test, and ctrl sample panels.

guide_efficiency

Vector of sgRNA feature names used.

guide_covariate_score

Matrix of sgRNA covariates.

guide_covariate_weight

Vector of sgRNA feature weights.

sample_response

Vector of inferred sample scaling factors.

gene_essentiality_likelihood

Data.table of likelihood values for all, all_null, test, test_null, ctrl, and ctrl_null tests.

gene_essentiality_low_CI

Lower confidence interval of gene essentiality estimates in gene_essentiality.

gene_essentiality_hi_CI

Higher confidence interval of gene essentiality estimates in gene_essentiality.

gene_essentiality_pvalue

Empirical p-values for within- and between-panel essentiality; data.table.

mean_var_model_parameters

Vector of inferred mean-variance relationship parameters; model specific.

Methods

Public methods

• ResultObj$new()

• ResultObj$clone()

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Method new()

Create ResultObj.

Usage

ResultObj$new(optObjList, DataObj, ModelObj)

Arguments

optObjList

List from optim fit. With null_liklihood, etc. added on.

DataObj

Produced from raw data. just need guide2gene_map and num_samples though.

ModelObj

Inferred parameteer object, just need mean_var_model.

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Method clone()

The objects of this class are cloneable with this method.

Usage

ResultObj$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

CshlSiepelLab/ACE documentation built on Sept. 10, 2021, 11:21 p.m.