readCufflinks {cummeRbund} | R Documentation

## readCufflinks

### Description

This initializes the backend SQLite table and provides a DB connection for all downstream data analysis.

### Usage

    readCufflinks(dir = getwd(), dbFile = "cuffData.db", gtfFile = NULL,
    				runInfoFile = "run.info", repTableFile = "read_groups.info",
    				geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", geneCount="genes.count_tracking", geneRep="genes.read_group_tracking",
    				isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_tracking", isoformRep="isoforms.read_group_tracking",
    				TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracking", TSSRep="tss_groups.read_group_tracking",
    				CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds.read_group_tracking",
    				CDSDiff = "cds.diff",
    				promoterFile = "promoters.diff",
    				splicingFile = "splicing.diff",
    				varModelFile = "var_model.info",
    				driver = "SQLite",
    				genome = NULL,
    				rebuild = FALSE,verbose=FALSE, ...)

### Arguments

`dir` | Directory in which all CuffDiff output files can be located. Defaults to current working directory.
`dbFile` | Name of backend database. Default is 'cuffData.db'
`gtfFile` | Path to .gtf file used in cuffdiff analysis. This file will be parsed to retrieve transcript model information.
`runInfoFile` | run.info file
`repTableFile` | read_groups.info file
`geneFPKM` | genes.fpkm_tracking file
`geneDiff` | gene_exp.diff file
`geneCount` | genes.count_tracking file
`geneRep` | genes.read_group_tracking file
`isoformFPKM` | isoforms.fpkm_tracking file
`isoformDiff` | isoform_exp.diff file
`isoformCount` | isoforms.count_tracking file
`isoformRep` | isoform.read_group_tracking file
`TSSFPKM` | tss_groups.fpkm_tracking file
`TSSDiff` | tss_group_exp.diff file
`TSSCount` | tss_groups.count_tracking file
`TSSRep` | tss_groups.read_group_tracking file
`CDSFPKM` | cds.fpkm_tracking file
`CDSExpDiff` | cds_exp.diff file
`CDSCount` | cds.count_tracking file
`CDSRep` | cds.read_group_tracking file
`CDSDiff` | cds.diff file (distribution tests on CDS)
`promoterFile` | promoters.diff file (distribution tests on promoters)
`splicingFile` | splicing.diff (distribution tests on isoforms)
`varModelFile` | varModel.info (emitted in cuffdiff >= v2.1)
`driver` | Driver for backend database. (Currently only "SQLite" is supported).
`genome` | A character string indicating to which genome build the .gtf annotations belong (e.g. 'hg19' or 'mm9')
`rebuild` | A logical argument to rebuild database backend.
`verbose` | A logical argument for super verbose reporting (As if it wasn't enough already!)
`...` | Additional arguments to readCufflinks

### Details

This is the initialization function for the cummeRbund package. It creates the SQLite backend database, populates the data, and provides a connection object for all future interactions with the dataset. Once the initial build is complete, this function will default to using the database for all future sessions. IMPORTANT: - Each R session should begin with a call to readCufflinks to re-open the connection to the database. - Should any connectivity issues to the database arise, another call to readCufflinks should create a new connection object and repair any issue. - The database can always be rebuild (using rebuild=TRUE) from the original CuffDiff output files.

### Value

A CuffSet object. A 'pointer' class that allows interaction with cufflinks/cuffdiff data via a SQLite database backend.

### Note

None.

### Author(s)

Loyal A. Goff

### References

None.

### Examples

    	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'

[Package cummeRbund version 2.34.0 Index]