getDE: Estimate Probability of Positive Log Ratio

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

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)

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