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

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.

Value

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

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.

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

Run this code

#Load cufflinks example data
cuffDB <- prepareCuffExample()

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

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