LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data

Package index
Search the LineagePulse package
Vignettes
Functions
271
Source code
24
Man pages
59
Home
/
Bioconductor
/
LineagePulse
/
accessors: LineagePulseObject accession methods

accessors: LineagePulseObject accession methods
In LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description Usage Arguments Value Author(s) Examples

Description

Get internal data of LineagePulse output object.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
dfAnnotationProc(objLP)

dfResults(objLP)

lsMuModelH0(objLP)

lsMuModelH1(objLP)

lsMuModelConst(objLP)

lsMuModelH0_NB(objLP)

lsMuModelH1_NB(objLP)

lsDispModelH0(objLP)

lsDispModelH1(objLP)

lsDispModelConst(objLP)

lsDispModelH0_NB(objLP)

lsDispModelH1_NB(objLP)

lsDropModel(objLP)

lsFitConvergence(objLP)

matCountsProc(objLP)

matWeights(objLP)

scaDFSplinesDisp(objLP)

scaDFSplinesMu(objLP)

strReport(objLP)

vecAllGenes(objLP)

vecConfoundersDisp(objLP)

vecConfoundersMu(objLP)

scaOmega(objLP)

boolFixedPopulations(objLP)

vecH0Pop(objLP)

vecNormConst(objLP)

strVersion(objLP)

strReport(objLP)

Arguments

objLP

(LineagePulse-Object) A LineagePulse output object to extract from.

Value

The internal data object specified by the function.

Author(s)

David Sebastian Fischer

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
   
lsSimulatedData <- simulateContinuousDataSet(
    scaNCells = 10,
    scaNConst = 2,
    scaNLin = 2,
    scaNImp = 2,
    scaMumax = 100,
    scaSDMuAmplitude = 3,
    vecNormConstExternal=NULL,
    vecDispExternal=rep(20, 6),
    vecGeneWiseDropoutRates = rep(0.1, 6))
objLP <- runLineagePulse(
    counts = lsSimulatedData$counts,
    dfAnnotation = lsSimulatedData$annot,
    strMuModel = "impulse")
# get hidden objects within LineagePulse object
dfAnnotationProc <- dfAnnotationProc(objLP)
dfResults <- dfResults(objLP)
lsMuModelH0 <- lsMuModelH0(objLP)
lsMuModelH1 <- lsMuModelH1(objLP)
lsMuModelConst <- lsMuModelConst(objLP)
lsMuModelH0_NB <- lsMuModelH0_NB(objLP)
lsMuModelH1_NB <- lsMuModelH1_NB(objLP)
lsDispModelH0 <- lsDispModelH0(objLP)
lsDispModelH1 <- lsDispModelH1(objLP)
lsDispModelConst <- lsDispModelConst(objLP)
lsDropModel <- lsDropModel(objLP)
lsFitConvergence <- lsFitConvergence(objLP)
matCountDataProc <- matCountsProc(objLP)
matWeights <- matWeights(objLP)
scaDFSplinesDisp <- scaDFSplinesDisp(objLP) 
scaDFSplinesMu <- scaDFSplinesMu(objLP) 
strReport <- strReport(objLP) 
vecAllGenes <- vecAllGenes(objLP) 
vecConfoundersDisp <- vecConfoundersDisp(objLP) 
vecConfoundersMu <- vecConfoundersMu(objLP) 
scaOmega <- scaOmega(objLP) 
boolFixedPopulations <- boolFixedPopulations(objLP)
vecH0Pop <- vecH0Pop(objLP) 
vecNormConst <- vecNormConst(objLP) 
strVersion <- strVersion(objLP)

LineagePulse documentation built on Nov. 8, 2020, 7:01 p.m.

Related to accessors in LineagePulse...

LineagePulse index
README.md LineagePulse

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close