quantify_dpcr
Read-only
Digital PCR (dPCR) partition counts to absolute concentration, with no standard curve. Positives and accepted partitions become lambda = -ln(1 - k/n), lambda becomes copies per uL through the partition volume and the dilution chain, and the confidence interval is carried on the lambda scale under any of eleven published binomial interval methods. Returns the dMIQE-2020 occupancy QC beside every reading, so a well with no positives, or one saturated past 95% occupancy, is reported as such rather than as a number.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| wells | Yes | the well table: `Well,Sample,Target,Positives,Partitions`. Instrument column names are accepted as they are printed (Bio-Rad's `AcceptedDroplets`, QIAcuity's `Valid partitions`), so a real export needs no renaming. | |
| _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. | |
| _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. | |
| ci_method | No | which binomial confidence interval is carried onto the lambda scale. Values: agresti-coull (Agresti–Coull), asymptotic (Asymptotic (normal approximation)), bayes (Bayes (Jeffreys prior, highest-density)), cloglog (Complementary log-log), exact (Exact (Clopper–Pearson)), logit (Logit), lrt (Likelihood ratio), probit (Probit), prop.test (Score test inverted, continuity-corrected), profile (Profile likelihood), wilson (Wilson score). Advanced. | wilson |
| volume_cv | No | coefficient of variation of the partition volume, as a percentage. Ignored under the `poisson` model. There is no universal value and inventing one would fabricate the exact quantity the correction consumes - the one figure this repo has a published source for is QuantStudio 3D chip (Majumdar 2017) at 3.03 %, and that paper says the vendor re-estimates it per chip rather than treating it as a platform constant. In %. Only applies when volume_model is normal or truncated. | |
| conf_level | No | confidence level for the interval. Advanced. | |
| ratio_target | No | the assay whose COPY NUMBER you want, named as it appears in the table's Target column. Leave it and `ratio_reference` unset and no copy number is reported at all — a guessed pair is a fabricated comparison. | |
| volume_model | No | how partition-volume SPREAD is handled (QP-5c). `poisson` is the standard estimator and assumes every partition holds the same volume. The two Poisson-Plus arms (Majumdar 2017) integrate the Poisson negative probability over a normal volume distribution and invert it: `normal` is the closed-form Eq (9), `truncated` the exact Eq (13) over a normal cut off at zero, which is the honest density because a partition cannot hold a negative volume. The spread biases the standard estimate DOWNWARD, hard at high occupancy and not at all at low. Values: poisson (Standard Poisson (no correction)), normal (Poisson-Plus, normal (Eq 9)), truncated (Poisson-Plus, truncated normal (Eq 13)). | poisson |
| dilution_factor | No | fold dilution applied to the sample before the reaction (2 = diluted 1:2). Advanced. | |
| ratio_reference | No | the assay it is measured against: the single-copy or known-ploidy reference, again by its Target name. | |
| merge_replicates | No | pool wells that share a sample and target before quantifying. Replicates of one measurement are one measurement, and pooling the COUNTS is the correct way to combine them, never averaging concentrations. | |
| reference_copies | No | copies of the REFERENCE target per genome. 2 is a diploid autosome, 1 a haploid or single-copy locus. Advanced. | |
| reaction_volume_ul | No | total reaction volume, for copies per reaction. In uL. | |
| template_volume_ul | No | volume of template added to the reaction. Left at 0 the sample-concentration row is omitted rather than guessed. In uL. Advanced. | |
| partition_volume_nl | No | mean volume of ONE partition. A per-platform constant, not a universal one (Bio-Rad QX200 approx 0.85 nL, QIAcuity 26k approx 0.34 nL, QuantStudio 3D approx 0.755 nL), and dMIQE 2020 requires it to be reported with the result. In nL. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| rows | Yes | one reading per well, or per pooled replicate group: occupancy, lambda with its interval, and every concentration the supplied volumes support | |
| count | Yes | how many readings were produced | |
| ratios | Yes | target-vs-reference copy number per sample, with the exact Poisson rate ratio and its interval rescaled onto the concentration scale the number is on. Empty when no assay pair was named — never a guessed pair | |
| flagged | Yes | readings carrying at least one dMIQE occupancy flag | |
| ciMethod | Yes | the interval method that produced the bounds: a CI without its method is not comparable | |
| confLevel | Yes | the confidence level every interval in `rows` was computed at | |
| volumeModel | Yes | how partition-volume spread was handled. `poisson` means it was not — a concentration without this is not comparable with one that was corrected | |
| volumeCvPercent | Yes | the volume spread the correction used, echoed for the same reason as the partition volume: it changed the number | |
| partitionVolumeNl | Yes | the partition volume the concentrations were computed at, echoed because dMIQE requires it to travel with the number |