Description Usage Arguments Details Value Examples
testHeterosis
Following categorization of Paschold 2012 (Genome Res.),
bin genes by their heterosis value. Tests are accomplished by contrasts (or similar)
1 | testHeterosis(contrast.stats, alpha = 0.05, parentIDs = c("p1", "p2"))
|
contrast.stats |
A dataframe containing the statistical output of contrasts between parents and the F1. This must contain the following columns, in this order:
|
alpha |
FDR threshold for determining significance |
parentIDs |
vector of length 2: the names of P1 and P2 respectively |
... |
Not currently in use |
Categorization is as follows: ##'
1. LP<H<HP, no heterosis (additive)
2. LP=H<HP, low parent (lp)
3. LP<H=HP, high parent(hp)
4. LP=HP=H, no significance (no DE)
5. LP<HP<H, above high parent, parents are diff expressed (ahb)
6. LP=HP<H, above high parent, parents are equal (ahb)
7. H<LP<HP, below low parent, parents are diff expressed (blp)
8. H<LP=HP, below low parent, parents are equal (blp)
9. Abiguous (ambig)
a dataframe where each row is one gene with the following columns:
1. geneID: the gene identifier
2. highParent: p1 or p2
3. order: the ranked order of p1, f1 and p2, separated by "."
4. category1: the category of each gene following Paschold 2012
4. category2: simplified category1 described in parentheses above
1 2 3 4 5 6 | ## Not run:
test<-testHeterosis(contrast.stats=contrast.stats,
alpha = 0.1,
parentIDs = c("FIL2","HAL2"))
## End(Not run)
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