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

### See Also

`getExpression`, `estimateHyperPar`, `estimateDE`

### 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 1.28.0 Index]