madSelect {synlet} | R Documentation |
Select hits basing on median +- k*MAD, by default k is three.
madSelect(masterPlate, dat, k = 3, treatment, control, outFile = FALSE, normMethod = "PLATE")
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. |
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?
Chung,N.etal. Medianabsolutedeviationtoimprovehitselectionforgenome- scale RNAi screens. J. Biomol. Screen. 13, 149-158 (2008).
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]]))