# robtest: Calls the robnb function to estimate the coefficients, and... In DiPhiSeq: Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

## 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

 `1` ```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

 ```1 2 3 4 5``` ```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)) ```

DiPhiSeq documentation built on May 2, 2019, 11:56 a.m.