buildModel {pram} | R Documentation

## Build transcript models from aligned RNA-seq data

### Description

Build transcript models from aligned RNA-seq data

### Usage

    buildModel(in_bamv, out_gtf, method = "plcf", nthreads = 1,
        tmpdir = NULL, keep_tmpdir = FALSE, cufflinks = "",
        stringtie = "", taco = "", cufflinks_ref_fa = "")

### Arguments

`in_bamv` | A character vector of input BAM file(s). If mode 'cf' or 'st' is used, only one input RNA-seq BAM file is allowed. Currently, PRAM only supports strand-specific paired-end data with the first mate on the right-most of transcript coordinate, i.e., 'fr-firststrand' by Cufflinks's definition.
`out_gtf` | An output GTF file of predicted transcript models
`method` | A character string defining PRAM's model building method. Current available methods are: plcf: pooling + cufflinks plst: pooling + stringtie cfmg: cufflinks + cuffmerge stmg: stringtie + merging cftc: cufflinks + taco cf: cufflinks st: stringtie Default: 'plcf'
`nthreads` | An integer defining the number of threads to-be-used. Default: 1
`tmpdir` | A character string defining the full name of a folder for saving temporary files. If not tmpdir is give, PRAM will use R's tempdir().
`keep_tmpdir` | Whether to keep temporary files afterwards. Default: False
`cufflinks` | Cufflinks executable. Required by mode 'plcf', 'cfmg', and 'cf'. For mode 'cfmg', executable files of Cuffmerge, Cuffcompare, and gtf_to_sam from the Cufflinks suite are assumed to be under the same folder as Cufflinks. All the executables are available to download for Linux http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz and MacOS http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz. Souce code can be obtained from http://cole-trapnell-lab.github.io/cufflinks/. Default: ”
`stringtie` | StringTie executable file. Required by mode 'plst', 'stmg', and 'st'. Executable can be downloaded for Linux http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.Linux_x86_64.tar.gz and MacOS http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.OSX_x86_64.tar.gz. Souce code can be obtained from https://ccb.jhu.edu/software/stringtie/. Default: ”
`taco` | TACO executable file. Required by mode 'cftc'. Executable can be downloaded for Linux https://github.com/tacorna/taco/releases/download/v0.7.0/taco-v0.7.0.Linux_x86_64.tar.gz and MacOS https://github.com/tacorna/taco/releases/download/v0.7.0/taco-v0.7.0.OSX_x86_64.tar.gz. Souce code can be obtained from https://tacorna.github.io. Default: ”
`cufflinks_ref_fa` | Genome reference fasta file for Cufflinks. If supplied, will be used for cufflinks's '–frag-bias-correct' and cuffmerge's '–ref-sequence' options. Default: ”

### Value

None

### Examples

    fbams = c(  system.file('extdata/bam/CMPRep1.sortedByCoord.clean.bam',
                            package='pram'),
                system.file('extdata/bam/CMPRep2.sortedByCoord.clean.bam',
                            package='pram') )

    foutgtf = tempfile(fileext='.gtf')

    ## assuming the stringtie binary is in folder /usr/local/stringtie-1.3.3/
    ## you can run buildModel() by the following example
    ##
    # buildModel(fbams, foutgtf, method='plst',
    #            stringtie='/usr/local/stringtie-1.3.3/stringtie')

[Package pram version 1.4.0 Index]