svaseq: A function for estimating surrogate variables for count based...
In steveneschrich/msva: Surrogate Variable Analysis

Description Usage Arguments Value Examples

This function is the implementation of the iteratively re-weighted least squares approach for estimating surrogate variables. As a by product, this function produces estimates of the probability of being an empirical control. This function first applies a moderated log transform as described in Leek 2014 before calculating the surrogate variables. See the function empirical.controls for a direct estimate of the empirical controls.

svaseq(
  dat,
  mod,
  mod0 = NULL,
  n.sv = NULL,
  controls = NULL,
  method = c("irw", "two-step", "supervised"),
  vfilter = NULL,
  B = 5,
  numSVmethod = "be",
  constant = 1
)

`dat`	The transformed data matrix with the variables in rows and samples in columns
`mod`	The model matrix being used to fit the data
`mod0`	The null model being compared when fitting the data
`n.sv`	The number of surogate variables to estimate
`controls`	A vector of probabilities (between 0 and 1, inclusive) that each gene is a control. A value of 1 means the gene is certainly a control and a value of 0 means the gene is certainly not a control.
`method`	For empirical estimation of control probes use "irw". If control probes are known use "supervised"
`vfilter`	You may choose to filter to the vfilter most variable rows before performing the analysis. vfilter must be NULL if method is "supervised"
`B`	The number of iterations of the irwsva algorithm to perform
`numSVmethod`	If n.sv is NULL, sva will attempt to estimate the number of needed surrogate variables. This should not be adapted by the user unless they are an expert.
`constant`	The function takes log(dat + constant) before performing sva. By default constant = 1, all values of dat + constant should be positive.

sv The estimated surrogate variables, one in each column

pprob.gam: A vector of the posterior probabilities each gene is affected by heterogeneity

pprob.b A vector of the posterior probabilities each gene is affected by mod

n.sv The number of significant surrogate variables

library(zebrafishRNASeq)
data(zfGenes)
filter = apply(zfGenes, 1, function(x) length(x[x>5])>=2)
filtered = zfGenes[filter,]
genes = rownames(filtered)[grep("^ENS", rownames(filtered))]
controls = grepl("^ERCC", rownames(filtered))
group = as.factor(rep(c("Ctl", "Trt"), each=3))
dat0 = as.matrix(filtered)

mod1 = model.matrix(~group)
mod0 = cbind(mod1[,1])
svseq = svaseq(dat0,mod1,mod0,n.sv=1)$sv
plot(svseq,pch=19,col="blue")