# Surrogate Variable Analysis

## Documentation for package ‘sva’ version 3.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ComBat | Adjust for batch effects using an empirical Bayes framework
ComBat_seq | Adjust for batch effects using an empirical Bayes framework in RNA-seq raw counts
empirical.controls | A function for estimating the probability that each gene is an empirical control
f.pvalue | A function for quickly calculating f statistic p-values for use in sva
fstats | A function for quickly calculating f statistics for use in sva
fsva | A function for performing frozen surrogate variable analysis as proposed in Parker, Corrada Bravo and Leek 2013
irwsva.build | A function for estimating surrogate variables by estimating empirical control probes
num.sv | A function for calculating the number of surrogate variables to estimate in a model
psva | A function for estimating surrogate variables with the two step approach of Leek and Storey 2007
qsva | A function for computing quality surrogate variables (qSVs)
read.degradation.matrix | A function for reading in coverage data from degradation-susceptible regions
ssva | A function for estimating surrogate variables using a supervised approach
sva | sva: a package for removing artifacts from microarray and sequencing data
sva.check | A function for post-hoc checking of an sva object to check for degenerate cases.
svaseq | A function for estimating surrogate variables for count based RNA-seq data.
sva_network | A function to adjust gene expression data before network inference
twostepsva.build | A function for estimating surrogate variables with the two step approach of Leek and Storey 2007