A master function containing each quality control processing step.
Value
processCounts_output, getCounts_output, sampleid_output, getAntigenCounts_output, getCountsQC_output
Examples
# \donttest{
# Example data supplied with the package
your_raw_data <- c(
system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR"),
system.file("extdata", "example_MAGPIX_plate2.csv", package = "SeroTrackR"),
system.file("extdata", "example_MAGPIX_plate3.csv", package = "SeroTrackR")
)
your_plate_layout <- system.file(
"extdata", "example_platelayout_1.xlsx", package = "SeroTrackR"
)
# Read serology data and plate layout
sero_data <- readSeroData(your_raw_data,"magpix")
#> PASS: File example_magpix_plate1.csv successfully validated.
#> PASS: File example_magpix_plate2.csv successfully validated.
#> PASS: File example_magpix_plate3.csv successfully validated.
plate_list <- readPlateLayout(your_plate_layout, sero_data)
#> Plate layouts correctly identified!
# Run full pipeline including classification
runQC(
sero_data = sero_data,
plate_list = plate_list
)
#> $processCounts_output
#> # A tibble: 2,304 × 6
#> Location Sample Plate Antigen Count Warning
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 A1 Blank1 plate1 EBP 150 0
#> 2 A1 Blank1 plate1 LF005 88 0
#> 3 A1 Blank1 plate1 LF010 184 0
#> 4 A1 Blank1 plate1 LF016 170 0
#> 5 A1 Blank1 plate1 MSP8 105 0
#> 6 A1 Blank1 plate1 RBP2b.P87 127 0
#> 7 A1 Blank1 plate1 PTEX150 85 0
#> 8 A1 Blank1 plate1 PvCSS 119 0
#> 9 A2 Blank2 plate1 EBP 142 0
#> 10 A2 Blank2 plate1 LF005 97 0
#> # ℹ 2,294 more rows
#>
#> $getCounts_output
#> # A tibble: 288 × 7
#> # Groups: Location [96]
#> Location Plate Sum Repeat Row Col QC_total
#> <chr> <chr> <dbl> <chr> <chr> <dbl> <chr>
#> 1 A1 plate1 0 sufficient beads A 1 pass
#> 2 A1 plate2 1 repeat A 1 fail
#> 3 A1 plate3 0 sufficient beads A 1 pass
#> 4 A10 plate1 0 sufficient beads A 10 pass
#> 5 A10 plate2 0 sufficient beads A 10 pass
#> 6 A10 plate3 0 sufficient beads A 10 pass
#> 7 A11 plate1 0 sufficient beads A 11 pass
#> 8 A11 plate2 0 sufficient beads A 11 pass
#> 9 A11 plate3 0 sufficient beads A 11 pass
#> 10 A12 plate1 0 sufficient beads A 12 pass
#> # ℹ 278 more rows
#>
#> $sampleid_output
#> # A tibble: 2,304 × 7
#> SampleID Location Plate Sample Antigen Count Warning
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 Blank1 A1 plate1 Blank1 EBP 150 0
#> 2 Blank1 A1 plate1 Blank1 LF005 88 0
#> 3 Blank1 A1 plate1 Blank1 LF010 184 0
#> 4 Blank1 A1 plate1 Blank1 LF016 170 0
#> 5 Blank1 A1 plate1 Blank1 MSP8 105 0
#> 6 Blank1 A1 plate1 Blank1 RBP2b.P87 127 0
#> 7 Blank1 A1 plate1 Blank1 PTEX150 85 0
#> 8 Blank1 A1 plate1 Blank1 PvCSS 119 0
#> 9 Blank2 A2 plate1 Blank2 EBP 142 0
#> 10 Blank2 A2 plate1 Blank2 LF005 97 0
#> # ℹ 2,294 more rows
#>
#> $getAntigenCounts_output
#> # A tibble: 2,304 × 7
#> # Groups: Location, Antigen, Count [929]
#> Location Antigen Count Plate Repeat QC_antigen SampleID
#> <chr> <chr> <dbl> <chr> <fct> <chr> <chr>
#> 1 A1 EBP 150 plate1 sufficient beads pass Blank1
#> 2 A1 EBP 142 plate2 sufficient beads pass Blank1
#> 3 A1 EBP 150 plate3 sufficient beads pass Blank1
#> 4 A1 LF005 88 plate1 sufficient beads pass Blank1
#> 5 A1 LF005 85 plate2 sufficient beads pass Blank1
#> 6 A1 LF005 95 plate3 sufficient beads pass Blank1
#> 7 A1 LF010 184 plate1 sufficient beads pass Blank1
#> 8 A1 LF010 218 plate2 sufficient beads pass Blank1
#> 9 A1 LF010 184 plate3 sufficient beads pass Blank1
#> 10 A1 LF016 170 plate1 sufficient beads pass Blank1
#> # ℹ 2,294 more rows
#>
#> $getCountsQC_output
#> # A tibble: 288 × 20
#> Location SampleID Plate EBP_Count EBP_QC LF005_Count LF005_QC LF010_Count
#> <chr> <chr> <chr> <dbl> <chr> <dbl> <chr> <dbl>
#> 1 A1 Blank1 plate1 150 pass 88 pass 184
#> 2 A1 Blank1 plate2 142 pass 85 pass 218
#> 3 A1 Blank1 plate3 150 pass 95 pass 184
#> 4 A10 S8 plate1 50 pass 62 pass 52
#> 5 A10 S8 plate2 50 pass 51 pass 78
#> 6 A10 S8 plate3 52 pass 70 pass 51
#> 7 A11 S9 plate1 67 pass 60 pass 78
#> 8 A11 S9 plate2 60 pass 59 pass 63
#> 9 A11 S9 plate3 50 pass 68 pass 80
#> 10 A12 S10 plate1 65 pass 50 pass 80
#> # ℹ 278 more rows
#> # ℹ 12 more variables: LF010_QC <chr>, LF016_Count <dbl>, LF016_QC <chr>,
#> # MSP8_Count <dbl>, MSP8_QC <chr>, PTEX150_Count <dbl>, PTEX150_QC <chr>,
#> # PvCSS_Count <dbl>, PvCSS_QC <chr>, RBP2b.P87_Count <dbl>,
#> # RBP2b.P87_QC <chr>, QC_total <chr>
#>
# }