svacor {enviGCMS} | R Documentation |
Surrogate variable analysis(SVA) to correct the unknown batch effects
Description
Surrogate variable analysis(SVA) to correct the unknown batch effects
Usage
svacor(xset, lv = NULL, method = "medret", intensity = "into")
Arguments
xset |
xcmsset object |
lv |
group information |
method |
parameter for groupval function |
intensity |
parameter for groupval function |
Details
this is used for reviesed version of SVA to correct the unknown batch effects
Value
list object with various components such raw data, corrected data, signal part, random errors part, batch part, p-values, q-values, mass, rt, Posterior Probabilities of Surrogate variables and Posterior Probabilities of Mod. If no surrogate variable found, corresponding part would miss.
See Also
Examples
## Not run:
library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(cdffiles)
xset <- group(xset)
xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
xset2 <- group(xset2, bw = 10)
xset3 <- fillPeaks(xset2)
df <- svacor(xset3)
## End(Not run)
[Package enviGCMS version 0.7.1 Index]