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

View source: R/geneset-camera.R

Test whether a set of genes is highly ranked relative to other genes in terms of differential expression, accounting for inter-gene correlation.

1 2 3 4 5 6 7 | ```
## Default S3 method:
camera(y, index, design, contrast = ncol(design), weights = NULL,
use.ranks = FALSE, allow.neg.cor=FALSE, inter.gene.cor=0.01, trend.var = FALSE,
sort = TRUE, ...)
## Default S3 method:
cameraPR(statistic, index, use.ranks = FALSE, inter.gene.cor=0.01, sort = TRUE, ...)
interGeneCorrelation(y, design)
``` |

`y` |
a numeric matrix of log-expression values or log-ratios of expression values, or any data object containing such a matrix.
Rows correspond to probes and columns to samples.
Any type of object that can be processed by |

`statistic` |
a numeric vector of genewise statistics. If |

`index` |
an index vector or a list of index vectors. Can be any vector such that |

`design` |
design matrix. |

`contrast` |
contrast of the linear model coefficients for which the test is required. Can be an integer specifying a column of |

`weights` |
numeric matrix of precision weights. Can be a matrix of the same size as |

`use.ranks` |
do a rank-based test ( |

`allow.neg.cor` |
should reduced variance inflation factors be allowed for negative correlations? |

`inter.gene.cor` |
numeric, optional preset value for the inter-gene correlation within tested sets. If |

`trend.var` |
logical, should an empirical Bayes trend be estimated? See |

`sort` |
logical, should the results be sorted by p-value? |

`...` |
other arguments are not currently used |

`camera`

and `interGeneCorrelation`

implement methods proposed by Wu and Smyth (2012).
`camera`

performs a *competitive* test in the sense defined by Goeman and Buhlmann (2007).
It tests whether the genes in the set are highly ranked in terms of differential expression relative to genes not in the set.
It has similar aims to `geneSetTest`

but accounts for inter-gene correlation.
See `roast`

for an analogous *self-contained* gene set test.

The function can be used for any microarray experiment which can be represented by a linear model.
The design matrix for the experiment is specified as for the `lmFit`

function, and the contrast of interest is specified as for the `contrasts.fit`

function.
This allows users to focus on differential expression for any coefficient or contrast in a linear model by giving the vector of test statistic values.

`camera`

estimates p-values after adjusting the variance of test statistics by an estimated variance inflation factor.
The inflation factor depends on estimated genewise correlation and the number of genes in the gene set.

By default, `camera`

uses `interGeneCorrelation`

to estimate the mean pair-wise correlation within each set of genes.
`camera`

can alternatively be used with a preset correlation specified by `inter.gene.cor`

that is shared by all sets.
This usually works best with a small value, say `inter.gene.cor=0.01`

.

If `interGeneCorrelation=NA`

, then `camera`

will estimate the inter-gene correlation for each set.
In this mode, `camera`

gives rigorous error rate control for all sample sizes and all gene sets.
However, in this mode, highly co-regulated gene sets that are biological interpretable may not always be ranked at the top of the list.

With `interGeneCorrelation=0.01`

, `camera`

will rank biologically interpetable sets more highly.
This gives a useful compromise between strict error rate control and interpretable gene set rankings.

`cameraPR`

is a "pre-ranked" version of `camera`

where the genes are pre-ranked according to a pre-computed statistic.

`camera`

and `cameraPR`

return a data.frame with a row for each set and the following columns:

`NGenes` |
number of genes in set. |

`Correlation` |
inter-gene correlation (only included if the |

`Direction` |
direction of change ( |

`PValue` |
two-tailed p-value. |

`FDR` |
Benjamini and Hochberg FDR adjusted p-value. |

`interGeneCorrelation`

returns a list with components:

`vif` |
variance inflation factor. |

`correlation` |
inter-gene correlation. |

The default settings for `inter.gene.cor`

and `allow.neg.cor`

were changed to the current values in limma 3.29.6.
Previously, the default was to estimate an inter-gene correlation for each set.
To reproduce the earlier default, use `allow.neg.cor=TRUE`

and `inter.gene.cor=NA`

.

Di Wu and Gordon Smyth

Wu, D, and Smyth, GK (2012). Camera: a competitive gene set test accounting for inter-gene correlation.
*Nucleic Acids Research* 40, e133.
http://nar.oxfordjournals.org/content/40/17/e133

Goeman, JJ, and Buhlmann, P (2007).
Analyzing gene expression data in terms of gene sets: methodological issues.
*Bioinformatics* 23, 980-987.

`rankSumTestWithCorrelation`

,
`geneSetTest`

,
`roast`

,
`fry`

,
`romer`

,
`ids2indices`

.

There is a topic page on 10.GeneSetTests.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
y <- matrix(rnorm(1000*6),1000,6)
design <- cbind(Intercept=1,Group=c(0,0,0,1,1,1))
# First set of 20 genes are genuinely differentially expressed
index1 <- 1:20
y[index1,4:6] <- y[index1,4:6]+1
# Second set of 20 genes are not DE
index2 <- 21:40
camera(y, index1, design)
camera(y, index2, design)
camera(y, list(set1=index1,set2=index2), design, inter.gene.cor=NA)
camera(y, list(set1=index1,set2=index2), design, inter.gene.cor=0.01)
# Pre-ranked version
fit <- eBayes(lmFit(y, design))
cameraPR(fit$t[,2], list(set1=index1,set2=index2))
``` |

```
NGenes Direction PValue
set1 20 Up 0.0003405277
NGenes Direction PValue
set1 20 Down 0.1362665
NGenes Correlation Direction PValue FDR
set1 20 0.008377344 Up 0.02193614 0.04387227
set2 20 -0.028307786 Down 0.17971264 0.17971264
NGenes Direction PValue FDR
set1 20 Up 0.0003405277 0.0006810555
set2 20 Down 0.1362664669 0.1362664669
NGenes Direction PValue FDR
set1 20 Up 0.000340695 0.0006813899
set2 20 Down 0.136297883 0.1362978834
```

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