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Viewing changes to man/readCufflinks.Rd

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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man/readCufflinks.Rd
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This initializes the backend SQLite table and provides a DB connection for all downstream data analysis.
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}
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\usage{
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readCufflinks(dir = getwd(), dbFile = "cuffData.db", geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSDiff = "cds.diff", promoterFile = "promoters.diff", splicingFile = "splicing.diff", driver = "SQLite", rebuild = FALSE, ...)
 
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readCufflinks(dir = getwd(), dbFile = "cuffData.db", gtfFile = NULL, 
 
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                                runInfoFile = "run.info", repTableFile = "read_groups.info",
 
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                                geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", geneCount="genes.count_tracking", geneRep="genes.read_group_tracking",
 
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                                isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_tracking", isoformRep="isoforms.read_group_tracking",
 
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                                TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracking", TSSRep="tss_groups.read_group_tracking",
 
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                                CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds.read_group_tracking",
 
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                                CDSDiff = "cds.diff",
 
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                                promoterFile = "promoters.diff", 
 
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                                splicingFile = "splicing.diff", 
 
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                                driver = "SQLite", 
 
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                                genome = NULL, 
 
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                                rebuild = FALSE,verbose=FALSE, ...)
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}
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%- maybe also 'usage' for other objects documented here.
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\arguments{
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  \item{dbFile}{
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Name of backend database. Default is 'cuffData.db'
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}
 
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  \item{gtfFile}{
 
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Path to .gtf file used in cuffdiff analysis. This file will be parsed to retrieve transcript model information.
 
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}
 
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  \item{runInfoFile}{
 
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run.info file
 
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}
 
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  \item{repTableFile}{
 
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read_groups.info file
 
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}
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  \item{geneFPKM}{
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genes.fpkm_tracking file
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}
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  \item{geneDiff}{
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gene_exp.diff file
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}
 
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  \item{geneCount}{
 
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genes.count_tracking file
 
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}
 
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  \item{geneRep}{
 
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genes.read_group_tracking file
 
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}
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  \item{isoformFPKM}{
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isoforms.fpkm_tracking file
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}
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  \item{isoformDiff}{
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isoform_exp.diff file
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}
 
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  \item{isoformCount}{
 
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isoforms.count_tracking file
 
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}
 
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  \item{isoformRep}{
 
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isoform.read_group_tracking file
 
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}
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  \item{TSSFPKM}{
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tss_groups.fpkm_tracking file
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}
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  \item{TSSDiff}{
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tss_group_exp.diff file
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}
 
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  \item{TSSCount}{
 
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tss_groups.count_tracking file
 
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}
 
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  \item{TSSRep}{
 
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tss_groups.read_group_tracking file
 
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}
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  \item{CDSFPKM}{
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cds.fpkm_tracking file
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}
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  \item{CDSExpDiff}{
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cds_exp.diff file
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}
 
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  \item{CDSCount}{
 
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cds.count_tracking file
 
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}
 
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  \item{CDSRep}{
 
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cds.read_group_tracking file
 
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}
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  \item{CDSDiff}{
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cds.diff file (distribution tests on CDS)
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}
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  \item{driver}{
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Driver for backend database. (Currently only "SQLite" is supported).
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}
 
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  \item{genome}{
 
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A character string indicating to which genome build the .gtf annotations belong (e.g. 'hg19' or 'mm9')
 
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}
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  \item{rebuild}{
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A logical argument to rebuild database backend.
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}
 
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  \item{verbose}{
 
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A logical argument for super verbose reporting (As if it wasn't enough already!)
 
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}
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  \item{\dots}{
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Additional arguments to readCufflinks
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}