Nothing
ssmdEffect.fn <-
function(ssmd.vec, criterion=c("mainType","subType"))
{
##**************************************************************************
## function to derive the type of effect size based on SSMD values
## Input
## ssmd.vec: a vector for SSMD value
## criterion: whether use the criterion for deriving the main effect type
## or the sub-type
## Author: Xiaohua Douglas Zhang, 2007
## Reference:
## Zhang XHD, 2011. Optimal High-Throughput Screening: Practical
## Experimental Design and Data Analysis for Genome-scale RNAi Research.
## Cambridge University Press, Cambridge, UK
##**************************************************************************
effectClass.vec <- rep( NA, length(ssmd.vec) )
if( criterion == "mainType" ) {
effectClass.vec[ ssmd.vec >= 1.645 ] <- "extra.Large+"
effectClass.vec[ ssmd.vec >= 1 & ssmd.vec < 1.645 ] <- "Large+"
effectClass.vec[ ssmd.vec > 0.25 & ssmd.vec < 1 ] <- "Medium+"
effectClass.vec[ ssmd.vec > 0 & ssmd.vec <= 0.25 ] <- "Small+"
effectClass.vec[ ssmd.vec == 0 ] <- "ZeroEfffect"
effectClass.vec[ ssmd.vec < 0 & ssmd.vec > -0.25 ] <- "Small-"
effectClass.vec[ ssmd.vec <= -0.25& ssmd.vec > -1 ] <- "Medium-"
effectClass.vec[ ssmd.vec <= -1 & ssmd.vec > -1.645] <- "Large-"
effectClass.vec[ ssmd.vec <= -1.645 ] <- "extra.Large-"
} else if ( criterion == "subType" ) {
effectClass.vec[ ssmd.vec >= 5 ] <- "ExtremelyStrong+"
effectClass.vec[ ssmd.vec >= 3 & ssmd.vec < 5 ] <- "VeryStrong+"
effectClass.vec[ ssmd.vec >= 2 & ssmd.vec < 3 ] <- "Strong+"
effectClass.vec[ ssmd.vec >= 1.645& ssmd.vec < 2 ] <- "FairlyStrong+"
effectClass.vec[ ssmd.vec >= 1.28 & ssmd.vec < 1.645 ] <- "Moderate+"
effectClass.vec[ ssmd.vec >= 1 & ssmd.vec < 1.28 ] <- "FairlyModerate+"
effectClass.vec[ ssmd.vec > 0.75 & ssmd.vec < 1 ] <- "FairlyWeak+"
effectClass.vec[ ssmd.vec > 0.50 & ssmd.vec <= 0.75 ] <- "Weak+"
effectClass.vec[ ssmd.vec > 0.25 & ssmd.vec <= 0.50 ] <- "VeryWeak+"
effectClass.vec[ ssmd.vec > 0 & ssmd.vec <= 0.25 ] <- "ExtremelyWeak+"
effectClass.vec[ ssmd.vec == 0 ] <- "ZeroEffect"
effectClass.vec[ ssmd.vec < 0 & ssmd.vec >= -0.25] <- "ExtremelyWeak-"
effectClass.vec[ ssmd.vec < -0.25 & ssmd.vec >= -0.50] <- "VeryWeak-"
effectClass.vec[ ssmd.vec < -0.50 & ssmd.vec >= -0.75] <- "Weak-"
effectClass.vec[ ssmd.vec < -0.75 & ssmd.vec > -1 ] <- "FairlyWeak-"
effectClass.vec[ ssmd.vec <= -1 & ssmd.vec > -1.28 ] <- "FairlyModerate-"
effectClass.vec[ ssmd.vec <= -1.28& ssmd.vec > -1.645] <- "Moderate-"
effectClass.vec[ ssmd.vec <= -1.645& ssmd.vec > -2 ] <- "FairlyStrong-"
effectClass.vec[ ssmd.vec <= -2 & ssmd.vec > -3 ] <- "Strong-"
effectClass.vec[ ssmd.vec <= -3 & ssmd.vec > -5 ] <- "VeryStrong-"
effectClass.vec[ ssmd.vec <= -5 ] <- "ExtremelyStrong-"
} else {
return("Error: criterion must be 'mainType' or 'subType'.")
}
if( sum(is.na(ssmd.vec)) > 0 ) effectClass.vec[ is.na(ssmd.vec) ] <- NA
effectClass.vec
}
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