two.stage: ~~function to do ... ~~

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/TwoStage.r

Description

Utility function for the "fdr" function in package mcp.project.

Usage

1
two.stage(sorted, q, m)

Arguments

sorted

~~Describe sorted here~~

q

~~Describe q here~~

m

~~Describe m here~~

Details

~~ If necessary, more details than the description above ~~

Value

~Describe the value returned If it is a LIST, use

comp1

Description of 'comp1'

comp2

Description of 'comp2'

...

Note

~~further notes~~

~Make other sections like Warning with Warning .... ~

Author(s)

~~who you are~~

References

~put references to the literature/web site here ~

See Also

~~objects to See Also as help, ~~~

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (sorted, q, m) 
{
    cat("Calling two.stage \n")
    flush.console
    q1 = q/(1 + q)
    stage.one = bh(sorted, q1, adjust = T, m = m)
    r = sum(stage.one$Pvals[["rejected"]])
    if (r == 0) {
        stage.one$Pvals[["adjusted.pvals"]] = 1
        return(stage.one)
    }
    else if (r == m) {
        stage.one$Pvals[["adjusted.pvals"]] = stage.one$Pvals[["adjusted.pvals"]][1]
        return(stage.one)
    }
    else {
        m0 = m - r
        output = bh(sorted = sorted, q = q1, m0 = m0, m = m)
        output$Pvals[["adjusted.pvals"]] = two.stage.adjust(sorted, 
            q)
        return(output)
    }
  }

mcp.project documentation built on May 31, 2017, 2:26 a.m.