readCufflinks: readCufflinks

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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'

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.