LineagePulseObject-class: Container class for LineagePulse output

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description

LineagePulse output and intermediate results such as model fits.

Slots

dfAnnotationProc

(data frame cells x meta characteristics) Annotation table which contains meta data on cells.

dfResults

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

lsDispModelH1

(list) Object containing description of gene-wise dispersion parameter models of H1.

lsDispModelH0

(list) Object containing description of gene-wise dispersion parameter models of H0.

lsDispModelConst

(list) Object containing description of gene-wise dispersion parameter models of constant model (necessary if H0 is not constant (mixture models)).

lsDispModelH1_NB

(list) Object containing description of gene-wise dispersion parameter models of H1 with NB noise model.

lsDispModelH0_NB

(list) Object containing description of gene-wise dispersion parameter models of H0 with NB noise model.

lsDropModel

(list)

lsMuModelH0

(list) Object containing description of gene-wise mean parameter models of H0.

lsMuModelH1

(list) Object containing description of gene-wise mean parameter models of H1.

lsMuModelConst

(list) Object containing description of gene-wise means parameter models of constant model (necessary if H0 is not constant (mixture models)).

lsMuModelH0_NB

(list) Object containing description of gene-wise mean parameter models of H0 with NB noise model.

lsMuModelH1_NB

(list) Object containing description of gene-wise mean parameter models of H1. with NB noise model.

lsFitConvergence

(list) Fitting reporter summary.

matCountsProc

(count matrix genes x cells) Sparse matrix of counts, non-observed values are NA.

matWeights

(numeric matrix cells x mixtures) Assignments of cells to mixtures.

scaDFSplinesDisp

(scalar) If strDispModelFull=="splines" or strDispModelRed=="splines", the degrees of freedom of the natural cubic spline to be used as a dispersion parameter model.

scaDFSplinesMu

(scalar) If strMuModel=="splines", the degrees of freedom of the natural cubic spline to be used as a mean parameter model.

strReport

(str) LineagePulse stdout report (log).

vecAllGenes

(vector of strings) All genes originally supplied, including all zero genes.

vecConfoundersDisp

(vector of strings number of confounders on dispersion) Confounders to correct for in dispersion batch correction model, are subset of column names of dfAnnotation which describe condounding variables.

vecConfoundersMu

(vector of strings number of confounders on mean) Confounders to correct for in mu batch correction model, are subset of column names of dfAnnotation which describe condounding variables.

scaOmega

(scalar) Regularisation parameter on entropy penalty on mixture weights. Needed for mixture model mode only.

boolFixedPopulations

Whether a population of cells is to be fixed to be assigned to a subset of centroids (RSA scenario). Needed for mixture model mode only.

vecNCentroidsPerPop

Number of centroids per population (RSA scenario). Needed for mixture model mode only.

vecH0Pop

(integer vector) Needed for mixture model mode only.

vecNormConst

(numeric vector length number of cells) Normalisation constants (library size factors) for each cell.

strVersion

(str) Version of LineagePulse that was run.

Author(s)

David Sebastian Fischer

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.