A function to select the best CV by combining the replicates in duplicates. The function has been build for up to to 3 replicates so far
best_CV_estimation(dataCV, slide_id, lab_replicates, cv_cut_off)A data frame
A character string containing the identifier of the data frame variable.
A numeric value indicating the number of lab replicates.
a numeric value for the CV cut off. Should be between 0-100
A data frame with the best CV's estimated
Select set of replicates with the best CV
dataC <- readr::read_csv(system.file("extdata",
"dataC.csv", package="protGear"))
#> Rows: 567 Columns: 11
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sampleID, antigen, iden
#> dbl (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## this file has 3 lab replicates and the default names
dataCV <- cv_estimation(dataC ,lab_replicates=3)
#> Warning: The replicates are as expected per sample per antigen
best_CV_estimation(dataCV,slide_id = "iden", lab_replicates = 3,
cv_cut_off = 20)
#> Adding missing grouping variables: `row`
#> # A tibble: 126 × 27
#> # Groups: row [126]
#> row antigen sampleID sample_ar…¹ meanX sdX sdX2_X3 sdX1_X3 sdX1_X2 CVX
#> <int> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 AMA1 0.0085 11 643. 98.5 70 69.3 139. 15.3
#> 2 2 AMA1 0.0255 8 699 52.6 74.2 33.9 40.3 7.52
#> 3 3 AMA1 0.076 5 633. 81.3 35.4 77.1 112. 12.8
#> 4 4 AMA1 0.23 2 1725. 60.5 32.5 84.8 52.3 3.51
#> 5 5 AMA1 0.73 19 2504. 119. 166. 61.5 105. 4.75
#> 6 6 AMA1 177.78 4 58262 709. 994. 383. 612. 1.22
#> 7 7 AMA1 19.75 10 64143. 353. 476. 367. 109. 0.55
#> 8 8 AMA1 2.19 16 9243 383. 528. 156. 372. 4.15
#> 9 9 AMA1 533 1 53180. 559. 117. 735. 619. 1.05
#> 10 10 AMA1 59.26 7 61601 894. 1078. 1111. 32.5 1.45
#> # … with 116 more rows, 17 more variables: CVX2_X3 <dbl>, CVX1_X3 <dbl>,
#> # CVX1_X2 <dbl>, cvCat_all <chr>, cvSelected_all <dbl>, iden <chr>,
#> # `1` <dbl>, `2` <dbl>, `3` <dbl>, x <chr>, meanX1_X2 <dbl>, meanX1_X3 <dbl>,
#> # meanX2_X3 <dbl>, meanSelected <dbl>, mean_best_CV <dbl>, best_CV <dbl>,
#> # best_CV_cat <chr>, and abbreviated variable name ¹sample_array_ID