# library(devtools)
# install_git("http://github.com/RGLab/MASTDataPackage")
# install_git('http://github.com/RGLab/MAST')
## Warning: multiple methods tables found for 'grep'
## Warning: multiple methods tables found for 'grepl'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'IRanges'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'IRanges'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'AnnotationDbi'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'AnnotationDbi'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'GenomeInfoDb'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'GenomeInfoDb'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'GenomicRanges'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'GenomicRanges'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'XVector'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'XVector'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'GenomicFeatures'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'GenomicFeatures'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'Biostrings'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'Biostrings'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'rtracklayer'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'rtracklayer'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'GenomicAlignments'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'GenomicAlignments'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'SummarizedExperiment'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'SummarizedExperiment'
zlm <- zlm.SingleCellAssay(~condition + cngeneson, sca, method = "bayesglm",
ebayes = TRUE, ebayesControl = list(method = "MLE", model = "H1"))
## Mean % Deviance
dataset | component | V1 |
---|---|---|
mdc | C | 1.650106 |
mdc | D | 4.869932 |
MAIT | C | 4.135422 |
MAIT | D | 5.282912 |
## % Deviance 90th Percentile
dataset | component | 90% |
---|---|---|
mdc | C | 4.392776 |
mdc | D | 9.364816 |
MAIT | C | 10.816661 |
MAIT | D | 13.380499 |
Top 100 DE genes between stimulated and non-stimulated MAIT cells.
Some of the activated MAITs have transcriptional profiles more similar to unactivated MAITS.
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
egid | chrmap | symbol |
---|---|---|
1831 | Xq22.3 | TSC22D3 |
5716 | Xq22.3 | PSMD10 |
122704 | 14q11.2 | MRPL52 |
3002 | 14q11.2 | GZMB |
51102 | 1p35.3 | MECR |
93974 | 1p35.3 | ATPIF1 |
## [1] 5.956767 3.843590
## quartz_off_screen
## 2
## mac version of flowJo workspace recognized.
## quartz_off_screen
## 2
## quartz_off_screen
## 2