bScore: Calculate B-score

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

Description

Calculate the B-score for plates belonging to the same master plate. Positive / negative controls are removed from the calculation.

Usage

bScore(masterPlate, dat, treatment, control, outFile = FALSE)

Arguments

masterPlate	a maste plate to be normalized
dat	synthetic lethal RNAi screen data
treatment	the treatment experiment condition in EXPERIMENT_MODIFICATION
control	the control experiment condition in EXPERIMENT_MODIFICATION
outFile	should calculated B-score files be written to the current folder? File names is (masterPlate).bscore.csv.

Value

A list contains B-score for each master plate, treatment plates are the first columns, followed by control plates

References

Brideau, C., Gunter, B., Pikounis, B. & Liaw, A. Improved statistical methods for hit selection in high-throughput screening. J. Biomol. Screen. 8, 634-647 (2003).

Examples

bscore.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)), bScore,
  exampleDat, control = "control", treatment = "treatment", simplify = FALSE)

Example output

Loading required package: ggplot2
---Processing PLATE:1031121---

1: 34257
Final: 33965.5
---Processing PLATE:1031122---

1: 35666
Final: 35464.75
---Processing PLATE:1031123---

1: 26858
Final: 26757
---Processing PLATE:1031613---

1: 33731
Final: 33589
---Processing PLATE:1031614---

1: 32981
2: 32617.25
Final: 32546.69
---Processing PLATE:1031615---

1: 37003
2: 36509
Final: 36360.38
---Processing PLATE:1031124---

1: 31513
Final: 31328
---Processing PLATE:1031125---

1: 31410
2: 30929.25
Final: 30825.19
---Processing PLATE:1031126---

1: 36548
Final: 36237
---Processing PLATE:1031616---

1: 29878
Final: 29687.5
---Processing PLATE:1031617---

1: 32490
2: 32105.75
Final: 32058.44
---Processing PLATE:1031618---

1: 31370
Final: 31128.5
---Processing PLATE:1031127---

1: 29221
2: 28929.5
Final: 28900.5
---Processing PLATE:1031128---

1: 34804.5
Final: 34676.25
---Processing PLATE:1031129---

1: 31836
Final: 31672.5
---Processing PLATE:1031619---

1: 32052
Final: 31876
---Processing PLATE:1031620---

1: 30885
Final: 30654.25
---Processing PLATE:1031621---

1: 34933
Final: 34627.75

synlet documentation built on Nov. 8, 2020, 6:48 p.m.