rankProdHits: Select hits by the rank product method

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

Description

Select hits by rank product methods by comparing treatment and control.

Usage

rankProdHits(masterPlate, dat, treatment, control, normMethod = "PLATE")

Arguments

masterPlate	the master plate to be analyzed
dat	synthetic lethal RNAi screen data
treatment	the treatment condition in EXPERIMENT_MODIFICATION
control	the control condition in EXPERIMENT_MODIFICATION
normMethod	normalization methods to be used. If "PLATE", the raw readouts are normalized by plate median, otherwise use provided control siRNA

Value

A list contains results by the rank product method for each master plate.

• MASTER_PLATE: location of siRNA

• pvalue_treat_lowerthan_cont: p-value for the hypothesis that treatment has lower normalized readout compared to control

• FDR_treat_lowerthan_cont: FDR value

• treat_cont_log2FC: log2 fold change of treatment / control

References

Breitling, R., Armengaud, P., Amtmann, A. & Herzyk, P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573, 83-92 (2004).

Hong, F. et al. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 22, 2825-2827 (2006).

Examples

rankp.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)),
  rankProdHits, exampleDat, control = "control", treatment = "treatment",
  simplify = FALSE)
rankp.c <- data.frame(do.call(rbind,
  lapply(names(rankp.res), function(x) rankp.res[[x]])))

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