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Read a Q-View report export (CSV or XLSX)

Source: R/read_qview_report.R
read_qview_report.Rd

[Experimental]

Usage

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

Arguments

path

Character. Path to a Q-View report export (.csv or .xlsx).

strip_prefix

Logical. If TRUE, reverse Q-View's internal naming convention via strip_qview_prefix(). 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", structured as the read_qview() return value, with these deviations. Container-only slots (manifest, segments) are zero-row tibbles; metadata$container_version is NA. The concentrations tibble carries one extra column, flag (NA / "<" / ">" / "incalculable"), relative to read_qview(). report_csv echoes the full export in file order (metadata preamble, blank spacer rows, the analyte header, then the data rows), whereas read_qview()'s report_csv holds only the unique report data lines.

Details

Parses one of the flat report files Q-View exports next to the native .Q-View container – the ..._auto_report or ..._auto_all-parameters_report export, as either .csv or .xlsx – and returns the same qview object read_qview() builds from the binary container. Use it when only the exports were kept and the original .Q-View project file is unavailable.

The export shares its report layout with the CLOB embedded in the binary container, so the two readers agree on concentrations and pixel intensities. Two behaviours differ from read_qview(), both to preserve information the study workflows rely on:

  • The plain "Reduced Concentration" point estimate (one row per sample, the value the exports headline) is captured with statistic == "reduced". read_qview() currently keeps only the per-replicate / summary concentration rows.

  • Out-of-range cells are preserved, not dropped: a "< 52.50" cell yields concentration = 52.50 with flag = "<", a "> 7700" cell flag = ">", and an "Incalculable ..." cell concentration = NA with flag = "incalculable". In-range cells carry flag = NA.

See also

read_qview(), read_qview_template().

Other qview-reader: read_qview(), read_qview_template()

Examples

path <- system.file("extdata", "example-report.csv",
                    package = "qviewparsR")
if (nzchar(path)) {
  qv <- read_qview_report(path)
  qv$concentrations
}
#> ✔ Parsed report export example-report.csv: 3 well groups x 3 analytes (8
#>   concentration rows).
#> ℹ Q-View Version: "3.13"
#> # A tibble: 8 × 10
#>   well_group sample_id well  replicate statistic analyte unit  concentration
#>   <chr>      <chr>     <chr>     <int> <chr>     <chr>   <chr>         <dbl>
#> 1 Cal 1      Cal 1     A1            1 replicate Ba      ng/mL         28.0 
#> 2 Cal 1      Cal 1     A1            1 replicate Bb      ug/mL          0.41
#> 3 Cal 1      Cal 1     A2            2 replicate Ba      ng/mL         NA   
#> 4 Cal 1      Cal 1     A2            2 replicate Bb      ug/mL          0.47
#> 5 N12345     N12345    A3           NA reduced   Ba      ng/mL          2.5 
#> 6 N12345     N12345    A3           NA reduced   Bb      ug/mL          0.05
#> 7 N23456     N23456    A4           NA reduced   Ba      ng/mL          0.31
#> 8 N23456     N23456    A4           NA reduced   Bb      ug/mL          0.42
#> # ℹ 2 more variables: dilution <dbl>, flag <chr>