| robtest {DiPhiSeq} | R Documentation |
Calls the robnb function to estimate the coefficients, and then construct the statistical tests for DD and DE. It works for a single gene. y1 and y2 are count vectors for a single gene. diphiseq calls this function to do the calculation for each gene. Normal users often don't need to use this function directly.
Description
Calls the robnb function to estimate the coefficients, and then construct the statistical tests for DD and DE. It works for a single gene. y1 and y2 are count vectors for a single gene. diphiseq calls this function to do the calculation for each gene. Normal users often don't need to use this function directly.
Usage
robtest(y1, log.depth1, y2, log.depth2, c.tukey.beta = 4, c.tukey.phi = 4)
Arguments
y1 |
counts from group 1. a vector. |
log.depth1 |
log(sequencing depths) for samples in group 1. a vector. |
y2 |
counts from group 2. a vector. |
log.depth2 |
log(sequencing depths) for samples in group 2. a vector. |
c.tukey.beta |
The c value for beta in Huber function. The default value, 4, is typically regarded as appropriate and should work for most datasets. |
c.tukey.phi |
The c value for phi in Huber function. The default value, 4, is typically regarded as appropriate and should work for most datasets. |
Value
A vector that contains the elements:
phi1: the estimated dispersion of sample group 1.
phi2: the estimated dispersion of sample group 2.
beta1: the estimated (log) expression of sample group 1.
beta2: the estimated (log) expression of sample group 2.
statistic.phi: the z statistic for DD.
statistic.beta: the z statistic for DE.
p.value.phi: the p value for DD.
p.value.beta: the p value for DE.
Examples
d1 <- runif(10, min=1, max=2)
d2 <- runif(15, min=1, max=2)
y1 <- rnbinom(10, size=1, mu=d1*50)
y2 <- rnbinom(15, size=1, mu=d2*50)
res <- robtest(y1, log(d1), y2, log(d2))