Read a .Q-View project file

Usage

read_qview(
  path,
  strip_prefix = FALSE,
  verbose = TRUE,
  call = rlang::caller_env()
)

Arguments

path: Character. Path to the .Q-View file.
strip_prefix: Logical. If TRUE, reverse Q-View's internal naming convention via strip_qview_prefix() so identifiers match the original well-assignment template. Default FALSE.
verbose: Logical. Print a short summary after parsing. Default TRUE.
call: The execution environment of the calling function. Used for error reporting; experts only.

Value

A list with class "qview" containing:

metadata: Named list: project, plate, image, imager, product, user, report_created, qview_version, template, container_version, file_path, parsed_at.
manifest: Tibble with one row per declared file entry (name, size_bytes, parent).
segments: Tibble of H2 segment byte ranges (segment, start, end, size).
analytes: Tibble: spot_number, analyte, unit, plus lod, lloq, uloq, assay_control_low, assay_control_high when reported.
well_groups: Tibble: well_group, sample_id, is_standard, is_negative, is_sample, is_control, well_type.
pixel_intensities: Long-format tibble of replicate readings: well_group, sample_id, well, replicate, analyte, unit, pixel_intensity, dilution.
summary_statistics: Long-format tibble of per-group averages, std-dev, and CV statistics: well_group, sample_id, statistic, analyte, value, unit.
concentrations: Long-format concentration tibble or NULL if the regression model is "Qualitative".
curve_fit: Tibble with analyte, regression_model, or NULL if not reported.
report_csv: Character vector of the raw CSV report lines, or NULL if no report was generated.
plate_layout: Tibble with one row per well: well, plate_row, plate_col, well_group, sample_id, well_type, dilution.

Details

Parses a .Q-View binary container (a chemiluminescent multiplex ELISA project file holding an embedded H2 database plus binary LOB segments) and extracts the assay data: project metadata, analyte panel with units, well-group sample assignments, per-well replicate pixel intensities, summary statistics, and (when present) the embedded CSV report.

The file format is reverse-engineered from public binary inspection: it begins with a plain-text manifest, followed by three concatenated H2 database segments. The fully-formatted report Q-View renders for the user is stored as a CLOB inside the main H2 segment. This parser scans the binary for that CLOB, reassembles it across H2 page boundaries (2048-byte pages), and parses it as CSV.

Parsing is done in pure R: no Java runtime, no H2 database driver, no system dependencies beyond a working R installation.

Examples

# A small synthetic .Q-View ships with the package:
path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path)
#> ✔ Parsed example.Q-View: 5 well groups x 3 analytes (20 replicate rows).
#> ℹ Q-View Version: "3.13"
qv
#> 
#> ── Q-View project: "Example ELISA project" ─────────────────────────────────────
#> • Plate: "Plate 1"
#> • Image: "example-plate (01 Jan 2024 12:00)"
#> • Imager: "#000000 (00000)"
#> • Product: "EXAMPLE-LOT"
#> • Software: v"3.13"
#> • Template: "example-template"
#> • Created: "01 Jan 2024 12:05"
#> 
#> ── Analytes (3) ──
#> 
#> Ba (ng/ml), Bb (ug/ml), Ref Spot (N/A)
#> 
#> ── Well groups (5) ──
#> 
#> • standard: 2
#> • negative: 1
#> • control: 1
#> • sample: 1
#> 
#> ── Data ──
#> 
#> • replicate rows: 20
#> • summary stat rows: 0
#> • concentrations: 4 rows
#> • curve fit: 3 analytes
qv$analytes
#> # A tibble: 3 × 8
#>   spot_number analyte  unit       lod    lloq  uloq assay_control_low
#>         <int> <chr>    <chr>    <dbl>   <dbl> <dbl>             <dbl>
#> 1           1 Ba       ng/ml  0.065    0.26    18.9                NA
#> 2           2 Bb       ug/ml  0.00051  0.0029   0.2                NA
#> 3           3 Ref Spot N/A   NA       NA       NA                5000
#> # ℹ 1 more variable: assay_control_high <dbl>
head(qv$pixel_intensities)
#> # A tibble: 6 × 8
#>   well_group sample_id well  replicate analyte unit  pixel_intensity dilution
#>   <chr>      <chr>     <chr>     <int> <chr>   <chr>           <dbl>    <dbl>
#> 1 ICal 1     ICal 1    A1            1 Ba      ng/ml            8671       NA
#> 2 ICal 1     ICal 1    A1            1 Bb      ug/ml           19982       NA
#> 3 ICal 1     ICal 1    A2            2 Ba      ng/ml           17838       NA
#> 4 ICal 1     ICal 1    A2            2 Bb      ug/ml           23848       NA
#> 5 N12345     N12345    A3            1 Ba      ng/ml            1200       NA
#> 6 N12345     N12345    A3            1 Bb      ug/ml            1300       NA

if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot(qv, type = "plate_map")
}

Usage

Arguments

Value

Details

See also

Examples