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

This function computes pairwise fold changes. It also works for logarithmic data.

1 |

`x` |
numeric vector. |

`g` |
grouping vector or factor |

`ave` |
function to compute the group averages. |

`log` |
logical. Is the data logarithmic? |

`base` |
If |

`mod.fc` |
logical. Return modified fold changes? (see details) |

`...` |
optional arguments to |

The function computes pairwise fold changes between groups, where
the group values are aggregated using the function which is
given by the argument `ave`

.

The fold changes are returned in a slightly modified form if mod.fc = TRUE.
Fold changes `FC`

which are smaller than `1`

are reported as
to `-1/FC`

.

The implementation is in certain aspects analogously to `pairwise.t.test`

.

Vector with pairwise fold changes.

Matthias Kohl [email protected]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
set.seed(13)
x <- rnorm(100) ## assumed as log2-data
g <- factor(sample(1:4, 100, replace = TRUE))
levels(g) <- c("a", "b", "c", "d")
pairwise.fc(x, g)
## some small checks
res <- by(x, list(g), mean)
2^(res[[1]] - res[[2]]) # a vs. b
-1/2^(res[[1]] - res[[3]]) # a vs. c
2^(res[[1]] - res[[4]]) # a vs. d
-1/2^(res[[2]] - res[[3]]) # b vs. c
-1/2^(res[[2]] - res[[4]]) # b vs. d
2^(res[[3]] - res[[4]]) # c vs. d
``` |

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