summary.DiscreteFDR {DiscreteFDR}R Documentation

Summarizing Discrete FDR Results

Description

summary method for class "DiscreteFDR"

Usage

## S3 method for class 'DiscreteFDR'
summary(object, ...)

## S3 method for class 'summary.DiscreteFDR'
print(x, max = NULL, ...)

Arguments

object

an object of class "DiscreteFDR".

...

further arguments passed to or from other methods.

x

an object of class "summary.DiscreteFDR".

max

numeric or NULL, specifying the maximal number of rows of the p-value table to be printed. By default, when NULL, getOption("max.print") is used.

Details

summary.DiscreteFDR objects include all data of an DiscreteFDR object, but also include an additional table which includes the raw p-values, their indices, the respective critical values (if present), the adjusted p-values (if present) and a logical column to indicate rejection. The table is sorted in ascending order by the raw p-values.

print.summary.DiscreteFDR simply prints the same output as print.DiscreteFDR, but also prints the p-value table.

Value

summary.DiscreteFDR computes and returns a list that includes all the data of an input DiscreteFDR, plus

Table

a data.frame, sorted by the raw p-values, that contains the indices, that raw p-values themselves, their respective critical values (if present), their adjusted p-values (if present) and a logical column to indicate rejection.

Examples

X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1)
X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2)
N1 <- rep(148, 9)
N2 <- rep(132, 9)
Y1 <- N1 - X1
Y2 <- N2 - X2
df <- data.frame(X1, Y1, X2, Y2)
df

#Construction of the p-values and their support
df.formatted <- fisher.pvalues.support(counts = df, input = "noassoc")
raw.pvalues <- df.formatted$raw
pCDFlist <- df.formatted$support

DBH.sd.crit <- DBH(raw.pvalues, pCDFlist, direction = "sd", ret.crit.consts = TRUE)
summary(DBH.sd.crit)


[Package DiscreteFDR version 1.3.6 Index]