getMeanVariance: Calculate mean and variance of expression samples

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Calculate mean and variance of expression samples or log-expression samples

Usage

getMeanVariance(sampleFiles, outFile, log=NULL, type=NULL, verbose=NULL,
      norm=NULL, pretend=FALSE)

Arguments

sampleFiles	Vector of one or more files containing the expression samples.
outFile	Name of the output file.
log	Use logged values.
type	Type of variance, possible values: sample,sqDif for sample variance or squared difference.
verbose	Verbose output.
norm	Vector of (multiplicative) normalization constants for library size normalization of expression samples. Number of constants has to match the number of expression samples files.
pretend	Do not execute, only print out command line calls for the C++ version of the program.

Details

The getMeanVariance function computes means and variances of MCMC expression samples. These can be computed either from single file or from multiple files using sample variance. Variance of two experiments (i.e. technical or biological replicates) can be estimated also by using sqDif option for type which specify the computation of the average square distance between the samples from two sets.

Value

.means

File containing means (first column) and variance (second column) for each transcript (or row in the sample files)

Author(s)

Peter Glaus

See Also

estimateExpression

Examples

setwd(system.file("extdata",package="BitSeq"));
sampleFileNames = c("data-c1b0.rpkm","data-c1b1.rpkm")
getMeanVariance(sampleFiles=sampleFileNames, outFile="data-c1.Lmean", log=1,
      norm=c(1.0017, 0.9998))

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.