Package 'WGCNA' - Laboratory Web Sites - UCLA

12 bicor
}
sep = ".")
NS1 = networkScreening(y = y, datME = datME, datExpr = datExpr)
ES = data.frame(cor(y, datME, use = "p"))
rr = max(abs(ES), na.rm = T)
AAcriterion = sqrt(length(y) - 2) * rr/sqrt(1 - rr^2)
ESy = (1 + max(abs(ES), na.rm = T))/2
ES = data.frame(ES, ESy = ESy)
ES.999 = as.numeric(as.vector(ES))
ES.999[!is.na(ES) & ES > 0.9999] = 0.9999
ES.pvalue = FisherTransformP(r = abs(ES.999), n = sum(!is.na(y)))
ES.pvalue[length(ES.999)] = 0
EigengeneSignificance.pvalue = data.frame(matrix(ES.pvalue,
nrow = 1))
names(EigengeneSignificance.pvalue) = names(ES)
datME = data.frame(datME, y = y)
names(ES) = paste("ES", substr(names(ES), 3, 100), sep = "")
print(signif(ES, 2))
output = list(networkScreening = data.frame(NS1, MMdata,
MMdataPvalue), datME = data.frame(datME), eigengeneSignificance = data.frame(ES),
eigengeneSignificance.pvalue = EigengeneSignificance.pvalue,
AAcriterion = AAcriterion)
output
bicor
Biweight Midcorrelation
Description
Calculate biweight midcorrelation efficiently for matrices.
Usage
bicor(x, y = NULL, robustX = TRUE, robustY = TRUE, use = "all.obs", verbose = 0,
Arguments
x
y
a vector or matrix-like numeric object
a vector or matrix-like numeric object
robustX use robust calculation for x
robustY use robust calculation for y
use
verbose
indent
specifies handling of NAs. One of (unique abbreviations of) "all.obs", "pairwise.complete.obs".
if non-zero, the underlying C function will print some diagnostics.
indentation for diagnostic messages. Zero means no indentation, each unit adds
two spaces.