cummeRbund (version 2.14.0)

readCufflinks: 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

Value

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

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.

References

None.

Examples

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