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_featuresGRanges 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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(spliceR)
Loading required package: cummeRbund
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: 'fastcluster'
The following object is masked from 'package:stats':
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: RColorBrewer
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:cummeRbund':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Attaching package: 'spliceR'
The following object is masked from 'package:cummeRbund':
conditions
The following object is masked from 'package:BiocGenerics':
conditions
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/spliceR/prepareCuff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: prepareCuff
> ### Title: Prepare assembled RNA-seq data from Cufflinks for spliceR
> ### Aliases: prepareCuff
>
> ### ** Examples
>
> #Load cufflinks example data
> cuffDB <- prepareCuffExample()
Creating database /tmp/RtmpHf9iM8/cuffData.db
Reading Run Info File /tmp/RtmpHf9iM8/run.info
Writing runInfo Table
Reading Read Group Info /tmp/RtmpHf9iM8/read_groups.info
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/RtmpHf9iM8/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /tmp/RtmpHf9iM8/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/RtmpHf9iM8/promoters.diff
Writing promoterDiffData table
Reading /tmp/RtmpHf9iM8/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /tmp/RtmpHf9iM8/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/RtmpHf9iM8/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /tmp/RtmpHf9iM8/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/RtmpHf9iM8/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /tmp/RtmpHf9iM8/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/RtmpHf9iM8/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /tmp/RtmpHf9iM8/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/RtmpHf9iM8/splicing.diff
Writing splicingDiffData table
Reading /tmp/RtmpHf9iM8/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /tmp/RtmpHf9iM8/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/RtmpHf9iM8/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /tmp/RtmpHf9iM8/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/RtmpHf9iM8/cds.diff
Writing CDSDiffData table
Reading /tmp/RtmpHf9iM8/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /tmp/RtmpHf9iM8/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped
5: attributes are not identical across measure variables; they will be dropped
6: attributes are not identical across measure variables; they will be dropped
7: attributes are not identical across measure variables; they will be dropped
8: attributes are not identical across measure variables; they will be dropped
>
> #Generate SpliceRList from cufflinks data
> cuffDB_spliceR <- prepareCuff(cuffDB)
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
Fixing cufflinks annotation problem...
Cufflinks annotation problem was fixed for 65 Cuff_genes
Creating spliceRList...
>
>
>
>
>
> dev.off()
null device
1
>