c212.BH.adjust.pvals {c212}

Benjamini-Hochberg procedure adjusted p-values

Description

Benjamini-Hochberg procedure adjusted p-values.

Usage

c212.BH.adjust.pvals(trial.data)

Arguments

trial.data

File or data frame containing the p-values for the hypotheses being tested. The data must include a column called p which contains the p-values of the hypotheses.

Value

Returns the original data frame, ordered by p, with an additional column p_adj.

Note

The adjusted p values may be directly compared to a value alpha to determine whether to declare a hypothesis significant under the Benjamini-Hochberg procedure at level alpha.

Note

No check is made for duplicate rows in the input file or data frame.

Author(s)

R. Carragher<[e-mail]>

References

D. V. Mehrotra and J. F. Heyse (2004). Use of the false discovery rate for evaluating clinical safety data. Stat Methods Med Res, 13(3):227–38, 2004.

Examples

trial.data <- data.frame(B = c(1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4),
j = c(1, 1, 2, 3, 4, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5),
AE = c("AE1", "AE2", "AE3", "AE4", "AE5", "AE6", "AE7", "AE8", "AE9", "AE10", "AE11",
"AE12", "AE13", "AE14", "AE15", "AE16", "AE17"),
p = c(0.135005, 0.010000, 0.001000, 0.005000, 0.153501, 0.020000, 0.0013, 0.0023,
0.011, 0.023000, 0.016, 0.0109, 0.559111, 0.751986, 0.308339, 0.837154, 0.325882))


adj <- c212.BH.adjust.pvals(trial.data)


## Not run: 
adj:
====
   B j   AE        p      p_adj
1  2 2  AE3 0.001000 0.01105000
2  3 2  AE7 0.001300 0.01105000
3  3 3  AE8 0.002300 0.01303333
4  2 3  AE4 0.005000 0.02125000
5  2 1  AE2 0.010000 0.02671429
6  3 7 AE12 0.010900 0.02671429
7  3 4  AE9 0.011000 0.02671429
8  3 6 AE11 0.016000 0.03400000
9  3 1  AE6 0.020000 0.03777778
10 3 5 AE10 0.023000 0.03910000
11 1 1  AE1 0.135005 0.20864409
12 2 4  AE5 0.153501 0.21745975
13 4 3 AE15 0.308339 0.39571386
14 4 5 AE17 0.325882 0.39571386
15 4 1 AE13 0.559111 0.63365913
16 4 2 AE14 0.751986 0.79898513
17 4 4 AE16 0.837154 0.83715400

## End(Not run)

adj[adj$p_adj <= 0.05, ]

## Not run: 
   B j   AE      p      p_adj
1  2 2  AE3 0.0010 0.01105000
2  3 2  AE7 0.0013 0.01105000
3  3 3  AE8 0.0023 0.01303333
4  2 3  AE4 0.0050 0.02125000
5  2 1  AE2 0.0100 0.02671429
6  3 7 AE12 0.0109 0.02671429
7  3 4  AE9 0.0110 0.02671429
8  3 6 AE11 0.0160 0.03400000
9  3 1  AE6 0.0200 0.03777778
10 3 5 AE10 0.0230 0.03910000

## End(Not run)