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

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

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]]))

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