gene_set_camera
Read-only
Competitive gene set test that accounts for inter-gene correlation (camera; Wu & Smyth 2012), as limma 3.68.5 runs it: is a set more differentially expressed than the genes outside it, with the variance of its mean statistic inflated by the correlation between its genes instead of treating them as independent.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | the tested coefficient by name; empty is the design's last. Only applies when statistic is voom. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| counts | No | a gene-by-sample table of raw read counts, gene IDs in the first column: camera then runs on its voom fit (filterByExpr, TMM, voom weights). Give this or `ranked`. Only applies when statistic is voom. | |
| design | No | with `counts`: the design formula, the variable of interest last. Only applies when statistic is voom. | ~ condition |
| ranked | No | a gene-wise statistic, 'gene statistic' per line (e.g. a DE run's Wald or moderated t). Only applies when statistic is ranked. | |
| samples | No | with `counts`: one row per sample, its name first, then the design's variables. Only applies when statistic is voom. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| contrast | No | 'factor, numerator, denominator', the denominator being the factor's reference level. Only applies when statistic is voom. | |
| geneSets | Yes | the gene sets, as GMT text (MSigDB, GO or WikiPathways exports): one set per line, tab-separated ID, description, then member gene IDs. IDs must be the same kind as the genes'. | |
| minCount | No | filterByExpr: minimum count in the smallest group's worth of samples. Only applies when statistic is voom. | |
| useRanks | No | a correlation-adjusted Wilcoxon rank-sum test instead of the parametric t on z-scores; robust to a few extreme genes. | |
| fdrCutoff | No | a set is called when its BH FDR (its p-value when one set is tested) is at most this. | |
| reference | No | reference level per factor, 'variable=level' separated by commas; a factor not named takes its alphabetically first level. Only applies when statistic is voom. | |
| statistic | No | ranked: cameraPR on a supplied gene-wise statistic (`ranked`). voom: camera on a voom fit of `counts` and `samples`, each gene's own residuals and weights. Given only `counts`, voom is assumed. | ranked |
| allowNegCor | No | with an estimated correlation: let a negative estimate deflate the variance (limma floors it at 0). Only applies when statistic is voom. | |
| directional | No | test up or down against the rest (true), or only whether the set's genes change more in either direction (false, a rank test on |statistic|). | |
| filterByExpr | No | drop genes too lowly expressed to test (edgeR's filterByExpr) before voom. Only applies when statistic is voom. | |
| interGeneCor | No | the fixed inter-gene correlation, limma's default 0.01 (a value most real sets exceed slightly). | |
| minTotalCount | No | filterByExpr: minimum total count. Only applies when statistic is voom. | |
| estimateCorrelation | No | with `counts`: estimate each set's correlation from the residuals instead of fixing it; the test then uses min(residual df, genes - 2) degrees of freedom. Only applies when statistic is voom. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| terms | Yes | every set with a member among the tested genes, by p: genes in the set, correlation, direction, p and BH FDR | |
| summary | Yes | the mode (voom camera or cameraPR), genes tested, sets supplied and tested, the degrees of freedom, the prior df of the variance squeeze, the settings limma changed | |
| enriched | Yes | the sets at or under the FDR cutoff |