Description Arguments Details References See Also Examples
Results for differential gene expression analysis using RNA-seq data simulated with the Polyester package from yeast data obtained from Schurch et al. (2016) as described in Korthauer and Kimes et al. (2019). Differential expression was tested using DESeq2.
metadata |
logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE) |
Results for this case study include:
polyester-results-null5
: null 5 vs. 5 comparison.
polyester-results-de5
: using unimodal alternative, 2000 DE genes, strong informative covariate, 5 vs. 5 comparison.
polyester-results-de5-uninfCov
: using unimodal alternative, 2000 DE genes, uninformative covariate, 5 vs. 5 comparison.
polyesterW-results-de5
: using unimodal alternative, 2000 DE genes, weak informative covariate, 5 vs. 5 comparison.
polyester-results-null10
: null 10 vs. 10 comparison.
polyester-results-de10
: using unimodal alternative, 2000 DE genes, strong informative covariate, 10 vs. 10 comparison.
polyester-results-de10-uninfCov
: using unimodal alternative, 2000 DE genes, uninformative covariate, 10 vs. 10 comparison.
polyesterW-results-de10
: using unimodal alternative, 2000 DE genes, weak informative covariate, 10 vs. 10 comparison.
Schurch, N. J. et al. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?. RNA, 22(6), 839-851.
1 2 3 4 5 6 7 8 9 10 11 12 13 | `polyester-results-de5`(metadata = TRUE)
## Not run:
`polyester-results-de5`()
`polyester-results-de5-uninfCov`()
`polyester-results-de10`()
`polyester-results-de10-uninfCov`()
`polyester-results-null5`()
`polyester-results-null10`()
`polyesterW-results-de5`()
`polyesterW-results-de10`()
## End(Not run)
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