extractNegLogPval {CNVScope} | R Documentation |
Finds the negative log p-value of a matrix, if it exists. Checks first to see if there is a p-value to return.
extractNegLogPval(x, y, repval = 300, lowrepval = 0, signed = F)
x |
a vector that is regressed in the fashion y~x. |
y |
a vector that is regressed in the fashion y~x. |
repval |
the replacement value if the regression cannot be performed, default 300 (the vectors are identical if this is used). |
lowrepval |
The low replacement value in the case that a regression p-value is undefined. |
signed |
change the sign of the negative log p-value based on the sign of beta? e.g. if the line has a negative slope, so will the returned value. If there is a positive slope, there will be a positive negative log p-value. if this option is disabled, then no sign changes will happen based on the sign of the slope. |
The negative log p-value or replacement value.
#small example xval<-c(1,1,1,1,1) yval<-c(1,2,3,4,5) a<-c(3,4,5,6,7) extractNegLogPval(x=xval,y=yval) #no possible p-value if one vector is constant. #Some edge cases this may not be correct (if the data lies near a constant), # but the indiviual sample data should reveal true trends. suppressWarnings(cor(xval,yval)) #you can't get a correlation value either. cor(a,a) #gives correlation of 1. extractNegLogPval(a,a) #gives replacement value. suppressWarnings(extractNegLogPval(x=a,y=yval)) #gives 107.3909 and warns about a nearly perfect fit.