R: Estimate Probability of Positive Log Ratio

getDE {BitSeq}

R Documentation

Estimate Probability of Positive Log Ratio

Description

Using expression samples, program estimates the probability of differential expression for each transcript.

Usage

getDE(conditions, outPrefix=NULL, samples=FALSE, trInfoFile=NULL, 
      norm=NULL, seed=NULL, pretend=FALSE )

Arguments

`conditions`	`List` of vectors, each vector containing names of files containing the expression samples from a replicate (Can be both technical and biological replicates. However, in order to get good results biological replicates for each condition are essential).
`outPrefix`	Prefix for the output files. Otherwise program creates temporary files, which are only valid for current R session.
`samples`	Produce samples of condition mean expression apart from PPLR and confidence.
`trInfoFile`	Transcript information file providing the names of transcripts.
`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.
`seed`	Sets the initial random seed for repeatable experiments.
`pretend`	Do not execute, only print out command line calls for the C++ version of the program.

Details

This function uses estimateHyperPar function to estimate the hyperparameters for DE model and the uses estimateDE function to infer the condition mean expression and calculate Probability of Positive Log Ratio.

Value

list with items:

`pplr`	`DataFrame` with PPLR and other statistics
`fn`	`list` with file names for PPLR file, `fn$pplr`, and condition mean expression samples, `fn$samplesFiles` (only with option `samples=TRUE`)

Author(s)

Peter Glaus

Examples

## Not run: 
cond1Files = c("data-c0b0.rpkm","data-c0b1.rpkm")
cond2Files = c("data-c1b0.rpkm","data-c1b1.rpkm")
deRes <- getDE( conditions=list(cond1Files, cond2Files))
## top 10 DE transcripts
head(deRes$pplr[ order(abs(0.5-deRes$pplr$pplr), decreasing=TRUE ), ], 10)

## End(Not run)

[Package BitSeq version 1.26.1 Index]