interactiontable: Returns a list of interactions with associated statistics.
In coRNAi: Analysis of co-knock-down RNAi data

Description Usage Arguments Value Warning Author(s) See Also Examples

This is a extanded wrapper around the topTable function from the limma package, as an option the ordinary t statistics can be calculated as well.

1	interactiontable(ebfit, sort = "none", ord.t = FALSE, correction = "BH")

`ebfit`	`ebfit` a MArrayLM object produced by the eBayes function
`sort`	character string specifying which statistic to rank genes by, possible arguments are none, ID,size, t,B,adj.P.val,P.Value, and if ord.t = TRUE: ord.t, ord.p and ord.p.adj.
`ord.t`	Logical, should ordinary t statistics be calculted? Default is FALSE.
`correction`	method used to adjust the p-values for multiple testing. Default is BH. See `p.adjust` for the complete list of options.

Returns a dataframe where the rows are the interaction pairs and the columns the statistics:

ID: Interaction pair if

size: the average interaction size

t: the moderated t statistics

P.Value: p-value for the moderated t statistics

adj.P.Val: adjusted p-value

B: the b statistics

if the ord.t=TRUE, the ordinary t statistics (ord.t), with correspnding p-values (ord.p) and adjusted p-values (ord.p.adj)

usage of the ordinary t statistics is not recommended for data sets with few replicates.

Elin Axelsson

p.adjust,topTable

## simulated data
     y <- matrix(rnorm(50*4,sd=1),50,4)
     rownames(y) <- paste("Pair",1:50)
    
     # fit and eBayes
     fit <- lmFit(y)
     fit <- eBayes(fit)
     tt = interactiontable(fit,sort="size")
     head(tt)