simulate_rnaseq_power
Read-only
Power and FDR for a two-group RNA-seq experiment by SIMULATION (PROPER 1.44.0): whole experiments drawn from a real pilot (Cheung, Gilad, Bottomly, MAQC, or a sequencing depth), each run through edgeR's exact test at every sample size.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | No | the seed; round i uses seed + i, as PROPER does. Advanced. | |
| genes | No | genes in the simulated experiment. | |
| pilot | No | where each gene's baseline expression comes from: one of PROPER's pilots, a sequencing depth applied to aggregated human expression, or one constant. Values: cheung (Cheung (unrelated people, large dispersion)), gilad (Gilad (human liver, moderate)), bottomly (Bottomly (inbred mice, small)), maqc (MAQC (technical replicates)), depth (Sequencing depth), constant (One constant). | cheung |
| _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. | |
| cutoff | No | the cut-off a gene is called at. | |
| rounds | No | simulated experiments. PROPER's own default is 100; each is a full edgeR run at every sample size, so time grows with it. | |
| strata | No | stratum break points; unset, PROPER's: 0, 10, 20, 40 … 1280, ∞ for expression. Advanced. | |
| target | No | which DE genes count as worth finding: by |log fold change|, or by |log fold change| / √dispersion. Values: lfc (Log fold change), effectsize (Effect size). | lfc |
| call_by | No | call a gene by its FDR or its raw p-value. Values: fdr (FDR), pval (raw p-value). | fdr |
| _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. | |
| log_mean | No | the natural-log mean count every gene shares. Only applies when pilot is constant. | |
| filter_by | No | drop the lowest expression strata before counting, and recompute BH over what is left. Values: none (Keep every gene), expr (Drop low expression). Advanced. | none |
| threshold | No | the threshold a DE gene's size must exceed to count. | |
| dispersion | No | one dispersion (BCV²) for every gene, instead of the pilot's; left unset, the pilot's own. Advanced. | |
| replicates | No | replicates per group at each sample size to evaluate. | |
| stratify_by | No | stratify the power by expression (mean normalized count) or by dispersion. Values: expr (Expression), dispersion (Dispersion). Advanced. | expr |
| second_group | No | replicates in the second group at each size, when the groups differ. Advanced. | |
| depth_factors | No | sequencing depth multipliers to re-weight power to. Advanced. | |
| dropped_strata | No | which strata (1-based) to drop. Only applies when filter_by is expr. Advanced. | |
| log_fold_change | No | one log fold change for every DE gene; left unset, PROPER's normal(0, 1.5) draws. Advanced. | |
| changed_fraction | No | the proportion of genes that are differentially expressed. | |
| dispersion_pilot | No | take dispersions from this pilot instead (with a depth or a constant baseline, Cheung's unless set). Advanced. | |
| reads_per_sample | No | total reads per sample. Only applies when pilot is depth. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| power | Yes | marginal power at each sample size | |
| strata | Yes | the stratum intervals the stratified readouts are over | |
| powerSE | Yes | the Monte-Carlo standard error of each marginal power | |
| rScript | Yes | the R that reproduces the run | |
| summary | Yes | per sample size: nominal and achieved FDR (or type I error), marginal power, mean true and false discoveries, false discovery cost | |
| seqDepth | Yes | marginal power re-weighted to each sequencing depth factor, per sample size | |
| stratifiedFDR | Yes | achieved FDR by stratum and sample size | |
| stratifiedPower | Yes | power by expression (or dispersion) stratum, one line per sample size |