prepareCuff: Prepare assembled RNA-seq data from Cufflinks for spliceR

In spliceR: Classification of alternative splicing and prediction of coding potential from RNA-seq data.

Description

Prepare assembled RNA-seq data from Cufflinks for spliceR.

Usage

prepareCuff(cuffDB, fixCufflinksAnnotationProblem=TRUE,removeNonChanonicalChr=TRUE)

Arguments

cuffDB	a cuffDB object, produced by cummeRbund. This object must have been generated with cummeRbund, using the gtf parameter (see example), for spliceR to extract transcript model and exon information.
fixCufflinksAnnotationProblem	Fixes problems with Cufflinks gene symbol annotation. Please see the vignette for additional information.
removeNonChanonicalChr	Removes non-canonical chromosome names.

Details

NB: prepareCuff is optimized to work with the cummeRbund vs v2.7.2 or later. Please check your version, and update if appropriate. Use prepareCuff to prepare a cummeRbund/Cufflinks DB object for use by spliceR (see example). Often, it's appropriate to prefilter cufflinks data after running prepareCuff with preSpliceRFilter to reduce overhead on downstream analyses.

Value

A SpliceRList containing a transcript_features GRanges object with the following additional metacolumns extracted from the cufflinks DB:

spliceR.isoform_id	Cufflinks unique isoform id
spliceR.sample_1	Sample 1 identifier
spliceR.sample_2	Sample 2 identifier
spliceR.gene_id	Cufflinks unique gene id
spliceR.CDS_id	Cufflinks unique CDS id
spliceR.gene_short_name	Cufflinks unique short gene name
spliceR.TSS_group_id	Cufflinks unique TSS id
spliceR.class_code	Cufflinks class code (see cufflinks documentation)
spliceR.nearest_ref_id	Nearest reference id
spliceR.length	Length of the transcript
spliceR.gene_status	Cufflinks gene quantification status
spliceR.gene_value_1	Gene FPKM value for sample 1
spliceR.gene_value_2	Gene FPKM value for sample 2
spliceR.gene_log2_fold_change	Log2 fold change of gene expression (sample2 / sample1)
spliceR.gene_p_value	P-value for differential testing of difference of gene expression between samples
spliceR.gene_q_value	Adjusted p-value for differential testing of difference of gene expression between samples
spliceR.gene_significant	Yes/no; yes if difference of gene expression is significant
spliceR.iso_status	Cufflinks isoform quantification status
spliceR.iso_value_1	Isoform FPKM value for sample 1
spliceR.iso_value_2	Isoform FPKM value for sample 2
spliceR.iso_log2_fold_change	Log2 fold change of isoform expression (sample2 / sample1)
spliceR.iso_p_value	P-value for differential testing of difference of isoform expression between samples
spliceR.iso_q_value	P-value for differential testing of difference of isoform expression between samples
spliceR.iso_significant	Yes/no; yes if difference of isoform expression is significant

and a exon_features GRanges object containing exon model information.

Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

References

Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.

Examples

#Load cufflinks example data
cuffDB <- prepareCuffExample()

#Generate SpliceRList from cufflinks data
cuffDB_spliceR <- prepareCuff(cuffDB)

spliceR documentation built on May 2, 2018, 2:50 a.m.