tTest: student's t-test basing on B-score

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

Description

Select hits by student's t-test using B-score from treatment and control plates.

Usage

tTest(masterPlate, bScore, numTreat, numCont)

Arguments

masterPlate	the master plate to be analyzed
bScore	normalized bScore
numTreat	number of treatment plates
numCont	number of control plates

Value

A list containing student's t-test for each master plate

• pvalue: p-value of the t-test

• Treat_Cont: difference in bscore: treatment - control

• p_adj: BH adjusted p-value

References

Birmingham, A. et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 6, 569-575 (2009).

Examples

bscore.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)), bScore,
  exampleDat, control = "control", treatment = "treatment", simplify = FALSE)
bscore.ttest  <- sapply(names(bscore.res), tTest, bscore.res, numTreat = 3,
  numCont = 3, simplify = FALSE, USE.NAMES = TRUE)
bscore.combined <- data.frame(do.call(rbind, lapply(names(bscore.ttest),
  function(x) if (!is.null(bscore.ttest[[x]])) {data.frame(MASTER_PLATE = x,
  siRNAs = rownames(bscore.ttest[[x]]), bscore.ttest[[x]])})))

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