readCufflinks {cummeRbund} | R Documentation |
This initializes the backend SQLite table and provides a DB connection for all downstream data analysis.
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, ...)
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 |
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.
A CuffSet object. A 'pointer' class that allows interaction with cufflinks/cuffdiff data via a SQLite database backend.
None.
Loyal A. Goff
None.
a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'