testHeterosis: Bin genes by heterosis categories

In jtlovell/limmaDE2: A pipeline for differential expression analyses in LIMMA

Description

testHeterosis Following categorization of Paschold 2012 (Genome Res.), bin genes by their heterosis value. Tests are accomplished by contrasts (or similar)

Usage

testHeterosis(contrast.stats, alpha = 0.05, parentIDs = c("p1", "p2"))

Arguments

contrast.stats	A dataframe containing the statistical output of contrasts between parents and the F1. This must contain the following columns, in this order: 1. geneID: the gene identifier 2. p1vf1.lfc: log2fold change of parent 1 vs. the f1 3. p2vf1.lfc: log2fold change of parent 2 vs. the f1 4. p1vp2.lfc: log2fold change of parent 1 vs. the parent 2 5. p1vf1.fdrp: fdr-transformed p.value of parent 1 vs. the f1 6. p2vf1.fdrp: fdr-transformed p.value of parent 2 vs. the f1 7. p1vp2.fdrp: fdr-transformed p.value of parent 1 vs. the parent 2
alpha	FDR threshold for determining significance
parentIDs	vector of length 2: the names of P1 and P2 respectively
...	Not currently in use

Details

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)

Value

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

Examples

## Not run: 
test<-testHeterosis(contrast.stats=contrast.stats,
  alpha = 0.1,
  parentIDs = c("FIL2","HAL2"))

## End(Not run)

jtlovell/limmaDE2 documentation built on May 20, 2019, 3:14 a.m.