synlet (version 1.2.2)

madSelect: Select hits basing on median +- k*MAD

Description

Select hits basing on median +- k*MAD, by default k is three.

Usage

madSelect(masterPlate, dat, k = 3, treatment, control, outFile = FALSE,
  normMethod = "PLATE")

Arguments

masterPlate

the master plate to analysis

dat

synthetic lethal RNAi screen data

k

cutoff for selecting hits, default is three

treatment

the treatment condition in EXPERIMENT_MODIFICATION

control

the control condition in EXPERIMENT_MODIFICATION

outFile

whether or not write the median normalized results

normMethod

normalization methods to be used. If "PLATE", the raw readouts are normalized by plate median, otherwise use median provided control siRNA.

Value

• A data.frame contains the hits selection results.
  • MASTER_PLATE: location of siRNA
  • treat_cont_ratio: ratio of treatment / control
  • treat_median: median value of treatment plates
  • control_median: median value of control plates
  • Hits: Is this siRNA a hit?

References

Chung,N.etal. Medianabsolutedeviationtoimprovehitselectionforgenome- scale RNAi screens. J. Biomol. Screen. 13, 149-158 (2008).

Examples

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