inst/doc/mDCAnalysis/mDCAnalysis.md

In RGLab/MASTdata: This is the data used for the MAST paper

title: 'MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data. mDC Analysis.' author: Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Alex Shalek, Martin Prlic, Peter Linsley, Raphael Gottardo date: "2015-05-26" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{mDC Analysis} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}

mDC Cell Maturation

## Version Okay

## (0.00153,0.279]   (0.279,0.445]   (0.445,0.633]   (0.633,0.845] 
##        1.207297        1.207297        1.207297        1.207297 
##    (0.845,1.08]     (1.08,1.36]     (1.36,1.66]     (1.66,2.01] 
##        1.207297        1.207297        1.207297        1.207297 
##      (2.01,2.4]      (2.4,2.84]     (2.84,3.34]      (3.34,3.9] 
##        1.207297        1.207297        1.278617        1.294579 
##      (3.9,4.54]     (4.54,5.26]     (5.26,6.07]     (6.07,6.99] 
##        1.420138        1.420138        1.653459        2.730194 
##     (6.99,10.5] 
##        4.296567

Fit zlm to stimulation and timepoint

Test for any time effect in LPS

In the LPS stimulation, testing for any time effect, when adjusting for ngeneson we detect 1359 differentially expressed genes. When we don't adjust for ngeneson, we detect 1996 genes.

Gene set enrichment analysis

##  [1] "(Intercept)"    "cngeneson"      "StimPAM"        "StimPIC"       
##  [5] "StimLPS:Time2h" "StimPAM:Time2h" "StimPIC:Time2h" "StimLPS:Time4h"
##  [9] "StimPAM:Time4h" "StimPIC:Time4h" "StimLPS:Time6h" "StimPAM:Time6h"
## [13] "StimPIC:Time6h"

##                     TERM             GOID include    coefficient    Stim
##    1:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time2h StimLPS
##    2:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time4h StimLPS
##    3:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time6h StimLPS
##    4: proteasome complex       GO:0000502    TRUE StimLPS:Time2h StimLPS
##    5: proteasome complex       GO:0000502    TRUE StimLPS:Time4h StimLPS
##   ---                                                                   
## 1004:      PEAKED_INFLAM    PEAKED_INFLAM    TRUE StimLPS:Time4h StimLPS
## 1005:      PEAKED_INFLAM    PEAKED_INFLAM    TRUE StimLPS:Time6h StimLPS
## 1006:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time2h StimLPS
## 1007:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time4h StimLPS
## 1008:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time6h StimLPS
##       variable        value component
##    1:        P 2.255322e-28         P
##    2:        P 0.000000e+00         P
##    3:        P 0.000000e+00         P
##    4:        P 3.945754e-04         P
##    5:        P 1.710842e-06         P
##   ---                                
## 1004:   disc_Z 4.542155e+00      disc
## 1005:   disc_Z 1.407052e+00      disc
## 1006:   disc_Z 1.816686e+01      disc
## 1007:   disc_Z 3.384424e+01      disc
## 1008:   disc_Z 2.573727e+01      disc

##                     TERM             GOID include    coefficient    Stim
##    1:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time2h StimLPS
##    2:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time4h StimLPS
##    3:     CORE_ANTIVIRAL   CORE_ANTIVIRAL    TRUE StimLPS:Time6h StimLPS
##    4: proteasome complex       GO:0000502    TRUE StimLPS:Time2h StimLPS
##    5: proteasome complex       GO:0000502    TRUE StimLPS:Time4h StimLPS
##   ---                                                                   
## 1004:      PEAKED_INFLAM    PEAKED_INFLAM    TRUE StimLPS:Time4h StimLPS
## 1005:      PEAKED_INFLAM    PEAKED_INFLAM    TRUE StimLPS:Time6h StimLPS
## 1006:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time2h StimLPS
## 1007:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time4h StimLPS
## 1008:   SUSTAINED_INFLAM SUSTAINED_INFLAM    TRUE StimLPS:Time6h StimLPS
##       variable        value component
##    1:        P 2.255322e-28         P
##    2:        P 0.000000e+00         P
##    3:        P 0.000000e+00         P
##    4:        P 3.945754e-04         P
##    5:        P 1.710842e-06         P
##   ---                                
## 1004:   disc_Z 4.542155e+00      disc
## 1005:   disc_Z 1.407052e+00      disc
## 1006:   disc_Z 1.816686e+01      disc
## 1007:   disc_Z 3.384424e+01      disc
## 1008:   disc_Z 2.573727e+01      disc

Residuals within significant modules

PCA of core antiviral residuals

Module scores

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Visualization of residual correlation over time in LPS

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.2831

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.7317

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.7317 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3218 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.401 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.2831

Correlations accounting for ngeneson

## [1] 377

## [1] 534

## [1] 193

## [1] 362

PC plot of residuals in LPS

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Fit PAM and PIC

Visualization of residual correlation over time in PAM

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6551

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.4775

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.4775 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6041 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3993 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6551

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Visualization of residual correlation over time in PIC

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8058

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8955

## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8955 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.5383 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3324 
## 
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8058

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RGLab/MASTdata documentation built on May 8, 2019, 5:52 a.m.