parseAlignment {BitSeq} | R Documentation

## Compute probabilities of alignments

### Description

Compute probability of alignments and save them into .prob file.

### Usage

    parseAlignment( alignFile, outFile, trSeqFile, inputFormat=NULL, trInfoFile=NULL,
          expressionFile=NULL, readsN=NULL, uniform=TRUE, limitA=NULL, lenMu=NULL,
          lenSigma=NULL, excludeSingletons=NULL, mateNamesDiffer=NULL,
          verbose=NULL, veryVerbose=NULL, procN=NULL, pretend=FALSE)

### Arguments

`alignFile` | File containing read alignments.
`outFile` | Name of the output file.
`inputFormat` | Input format: possible values `SAM`, `BAM`. (This should be detected automatically in most cases.)
`trInfoFile` | File to save transcript information extracted from [BS]AM file and reference.
`trSeqFile` | File containing transcript sequence in FASTA format.
`expressionFile` | Transcript relative expression estimates — for better non-uniform read distribution estimation.
`readsN` | Total number of reads. This is usually not necessary if SAM/BAM contains also reads with no valid alignments.

`uniform` | Use uniform read distribution.
`limitA` | Limit maximum number of alignments per read. Reads with more alignments than limit will be discarded.
`lenMu` | Set mean of log fragment length distribution. l_frag ~ LogNormal(mu,sigma^2)
`lenSigma` | Set sigma^2 (or variance) of log fragment length distribution. l_frag ~ LogNormal(mu,sigma^2)

`excludeSingletons` | Exclude single mate alignments for paired-end reads.
`mateNamesDiffer` | Mates from paired-end reads have different names.
`verbose` | Verbose output.
`veryVerbose` | Very verbose output.
`procN` | Maximum number of threads to be used.
`pretend` | Do not execute, only print out command line calls for the C++ version of the program.

### Details

This function uses the alignments and reference file to assign probability to each alignment. It uses either bias-corrected or uniform model for the read distribution, assumes Log-Normal distribution of fragment lengths for pair-end read data and uses quality scores and mismatches to assign probability for every alignment of a read (or fragment) to a transcript.

### Value

`.prob` | file containing the alignment probabilities
`.tr` | file containing reference transcript names, lengths and effective lengths - optional

### Author(s)

Peter Glaus

### See Also

`estimateExpression`

### Examples

    ## Not run:
    parseAlignment(alignFile="data.sam", outFile="data.prob",
          trSeqFile="trReference.fa" ,trInfoFile="data.tr")

    ## End(Not run)

[Package BitSeq version 1.24.0 Index]