Description Usage Arguments Details Value Examples

`pipeDESeq2`

Run a pipeline of DESeq2 functions for differential
gene expression.

1 2 3 4 5 6 | ```
pipeDESeq2(counts, info, formula = NULL, reduced = NULL, testNames = NULL,
contrasts = NULL, contrastFormula = NULL, contrastNames = NULL,
returnNormData = "none", geneIDs = NA, verbose = TRUE,
fitType = "parametric", quiet = TRUE, betaPrior = F,
modelMatrixType = "standard", parallel = F, minReplicatesForReplace = 7,
...)
``` |

`counts` |
A count matrix, row names should be gene IDs |

`info` |
An experimental design matrix |

`formula` |
If specified, perform a likelihood ratio test. A vector of character strings that can be coerced into a formula. Must be of the same length as reduced. Specifies base formulas for LRT. |

`reduced` |
A character vector of the same length as formula, which can be coerced to a formula that represents a sub model to formula. All reduced formulae must be sub models of the respective formula. |

`testNames` |
A character string of names for the LRT, if specified, must be the same length as formula and reduced. |

`contrasts` |
A list of character vectors that can be input into DESeq2::results contrasts argument. |

`contrastFormula` |
The formula specifying the design matrix for the contrasts. Keep in mind that this formula specifies how the model is fit and can affect inference of the effects of contrasts. |

`contrastNames` |
Names for the contrasts. Must be the same length as contrasts |

`returnNormData` |
If NULL (default), no transformed data is returned. Other options are "rlog" and "vst" which return rlog and variance stabilized data respecitvel. |

`geneIDs` |
The names of genes. If NA, use row names from counts matrix |

`verbose` |
Logical, return progress updates? |

`fitType` |
Passed to DESeq. Default is "parametric" |

`quiet` |
Should messages from DESeq2 be suppressed? |

`betaPrior` |
Passed to DESeq. Default is F |

`modelMatrixType` |
Passed to DESeq. Default is "standard" |

`parallel` |
Passed to DESeq. Default is F |

`minReplicatesForReplace` |
Passed to DESeq. Default is 7 |

`...` |
additional arguments to pass to DESeq2::results |

This function runs the following pipeline:

1. DESeq's pipeline using the specified test

2. Extraction of results (from DESeq2::results)

3. Renaming of columns and combining results across tests

a list with 3 elements (if test is not run, elements are NULL):

1. "LRT_results": The results from the likelihood ratio tests

2. "CONT_results": The results from the contrasts

3. "normData": normalized data

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
## Not run:
library(deTools)
data(counts)
data(info)
stats<-pipeDESeq2(counts=counts, info=info,
formula = c(" ~ trt"),
reduced = c(" ~ 1"),
testNames = c("trt"))
stats<-pipeDESeq2(counts=counts, info=info,
contrastFormula = " ~ trt + geno",
contrasts = list(c("geno","HAL2","FIL2")),
contrastNames = "HvF")
stats<-pipeDESeq2(counts=counts, info=info,)
stats<-pipeDESeq2(counts=counts, info=info,
formula = c(" ~ trt + geno + trt:geno"," ~ trt + geno", " ~ trt + geno"),
reduced = c(" ~ trt + geno"," ~ trt"," ~ geno"),
testNames = c("GxE","geno","trt"),
contrastFormula = " ~ trt + geno",
contrasts = list(c("trt","Wet","Dry"),c("geno","HAL2","FIL2")),
contrastNames = c("WvD","HvF"),returnNormData = "vst")
## End(Not run)
``` |

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