ImpulseDE2Object-class {ImpulseDE2}R Documentation

Container class for ImpulseDE2 output

Description

ImpulseDE2 output and intermediate results such as model fits.

Slots

dfDEAnalysis

(data frame samples x reported characteristics) Summary of fitting procedure and differential expression results for each gene.

Entries only present in case-only DE analysis:

Entries only present in case-control DE analysis:

Entries only present if boolIdentifyTransients is TRUE:

vecDEGenes

(list number of genes) Genes IDs identified as differentially expressed by ImpulseDE2 at threshold scaQThres.

lsModelFits

(list length number of conditions fit (1 or 3)) 'case' or 'case', 'control', 'combined' One model fitting object for each condition: In case-only DE analysis, only the condition 'case' is fit. In case-control DE analysis, the conditions 'case', 'control','combined are fit. Each condition entry is a list of model fits for each gene. Each gene entry is a list of model fits to the individual models: Impulse model and constant model (if boolFitConst is TRUE). At this level, the sigmoid model fit can be added later. Each model fit per gene is a list of fitting parameters and results.

matCountDataProc

(matrix genes x samples) [Default NULL] Read count data, unobserved entries are NA. Processed matrix.

dfAnnotationProc

(data frame samples x covariates) Sample, Condition, Time (numeric), TimeCateg (str) (and confounding variables if given). Annotation table with covariates for each sample. Processed table.

vecDispersions

(numeric vector number of samples) Gene-wise negative binomial dispersion hyper-parameters.

vecSizeFactors

(numeric vector number of samples) Model scaling factors for each sample which take sequencing depth into account (size factors).

boolCaseCtrl

(bool) Whether to perform case-control analysis. Does case-only analysis if FALSE.

vecConfounders

(vector of strings number of confounding variables) Factors to correct for during batch correction. Have to supply dispersion factors if more than one is supplied. Names refer to columns in dfAnnotation.

scaNProc

(scalar) Number of processes for parallelisation.

scaQThres

(scalar) FDR-corrected p-value cutoff for significance.

strReport

(str) ImpulseDE2 stdout report.

Author(s)

David Sebastian Fischer


[Package ImpulseDE2 version 1.10.0 Index]