detectionPoobEcdf2 {sesame} | R Documentation |
aka pOOBAH2 (p-vals by Out-Of-Band Array Hybridization)
detectionPoobEcdf2( sdf, return.pval = FALSE, combine.neg = TRUE, pval.threshold = 0.05 ) pOOBAH2(sdf, return.pval = FALSE, combine.neg = TRUE, pval.threshold = 0.05)
sdf |
a |
return.pval |
whether to return p-values, instead of a
masked |
combine.neg |
whether to combine negative control probes with the out-of-band probes in simulating the signal background |
pval.threshold |
minimum p-value to mask |
The function takes a SigDF
as input, computes detection p-value
using out-of-band probes empirical distribution and returns a new
SigDF
with an updated mask slot.
The difference between this function and the original pOOBAH is that pOOBAH2 is based on background-subtracted and dyebias corrected signal and do not distinguish the color channel difference.
a SigDF
, or a p-value vector if return.pval is TRUE
sdf <- sesameDataGet("EPIC.1.SigDF") sum(sdf$mask) sdf <- detectionPoobEcdf2(sdf) sum(sdf$mask) sdf <- sesameDataGet("EPIC.1.SigDF") sum(sdf$mask) sdf <- pOOBAH2(sdf) sum(sdf$mask)