RiboVIEW-package: Visualization, quality control and statistical analysis of...

In carinelegrand/RiboVIEW: Visualization, Quality and Statistics for Ribosome Profiling

Description

Tools to visualize ribosome profiling (RiboMine) and to perform robust statistic and quality control of the data (RiboQC). We offer the user a webpage view to scan own data on the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drugs-related artifacts; codon enrichment including variability observed between mRNAs/positions for A, P and E sites; mining of causal or confounding factors.

This is a template workflow corresponding to the package vignette Intro_RiboVIEW.pdf. The package vignette contains additional information such as command results, plots, and explanations. The following R command :

'vignette("Intro_RiboVIEW")'

can be used to display the vignette.

Examples

# Sequenced reads aligned to mRNA (and containing no rRNA, depleted previously),
#   in bam format
readsBAM.1.1  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep1.bam",sep="")
readsBAM.1.2  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep2.bam",sep="")
readsBAM.1.3  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep3.bam",sep="")
readsBAM.2.1  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep1.bam",sep="")
readsBAM.2.2  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep2.bam",sep="")
readsBAM.2.3  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep3.bam",sep="")

list.bam <- list(readsBAM.1.1, readsBAM.1.2, readsBAM.1.3, 
                 readsBAM.2.1, readsBAM.2.2, readsBAM.2.3)


#
## Experimental conditions, in text and as indicators :
#    0 for control
#    1 for a condition, treatment, case, etc...
#    2, 3, etc. for further conditions

XP.conditions   <- c("cond1","cond1","cond1","cond2", "cond2","cond2")
XP.conditions.i <- c( 1,1,1,2,2,2)
XP.names        <- c("C1.R1", "C1.R2", "C1.R3", 
                     "C2.R1", "C2.R2", "C2.R3")

#
## Reference annotation for mRNAs' CDS.
#

refCDS <- paste(system.file(package="RiboVIEW", mustWork = TRUE), "/extdata/synth.tsv", sep="")
# Note : CDS annotation can be obtained from a GTF file, 
#        using gtf2table(my-gtf-file, outfile = my-cds-file)
#        (for example GTF file as provided by Ensembl.org work well with gtf2table)

#
## Reference sequences for mRNAs.
#

refFASTA <- paste(system.file(package="RiboVIEW", mustWork = TRUE), "/extdata/synth.fasta", sep="")

#
## Work and output folder.
#

pathout  <-  paste(tempdir(),"/", sep="")
  ## !! This is a temporary directory, which will be erased when you leave R !!
  ##   For your own analyses you would probably prefer to point to a permanent repository :
  #      pathout <- /home/me/address-to-my-output-repository/ # Define address, 
  #                                                   #including a final slash.
  #      system(paste('mkdir',pathout)) # Create folder at said address.
  #      setwd(pathout)  # Go to this directory. This is useful if you want to 
  #                                         #save additional tables or figures.

# 
## A-site coverage periodicity by length
#

periodicity(list.bam, refCDS, refFASTA, pathout, XP.names, versionStrip = FALSE)

# 
## Select footprint length with sufficient periodicity
#

attach(listminmax <- select.FPlen(list.bam, pathout, XP.names))

#
## Codon occupancy, codon enrichment.
# 

enrichmentNoccupancy(list.bam, refCDS, refFASTA, mini, maxi, XP.names,  
                       pathout, versionStrip = FALSE)
 
#
## Visualisation.
#

generate.m.s(XP.conditions, XP.names, pathout, B=1000)

visu.m.s.enrichmnt.res <- visu.m.s.enrichmnt(XP.conditions, XP.names, pathout)
visu.m.s.enrichmnt.res

visu.tracks.res <- visu.tracks(XP.conditions, XP.names, pathout, refCDS, 
                               mRNA="random", 
                               codon.labels=FALSE, codon.col="darkslateblue")
visu.tracks.res

Venn.all.res <- Venn.all(XP.names, pathout)
Venn.all.res

enricht.aroundA.res <- enricht.aroundA(XP.conditions, 
  XP.names, pathout)
enricht.aroundA.res


#
## Replicates.
#

repl.correl.counts.Venn.res <- repl.correl.counts.Venn(XP.conditions, XP.names, 
                                                       pathout)
repl.correl.counts.Venn.res

repl.correl.gene.res <- repl.correl.gene(XP.conditions, XP.names, pathout)
repl.correl.gene.res

repl.correl.codon.res <- repl.correl.codon(list.bam, refCDS, refFASTA, 
                                           mini, maxi, 
                                           XP.names, XP.conditions, pathout)
repl.correl.codon.res

repl.correl.heatmap.res <- repl.correl.heatmap(XP.conditions.i, XP.names, pathout)
repl.correl.heatmap.res

#
## Potential artefacts due to Cycloheximide or other drugs
#

chx.artefacts.res <- chx.artefacts(XP.conditions, XP.names, pathout)
chx.artefacts.res

#
## Nucleotide and codon frequency at footprint boundaries.
#

ntcodon.freq.nt.res <- ntcodon.freq.nt(XP.conditions, XP.names, pathout)
ntcodon.freq.nt.res

ntcodon.freq.cod.res <- ntcodon.freq.cod(XP.conditions, XP.names, pathout)
ntcodon.freq.cod.res

#
## Batch effects
#

batch.effects.lm.e.res <- batch.effects.lm.e(XP.conditions, XP.names, pathout)
batch.effects.lm.e.res

batch.effects.pca.res <- batch.effects.pca(XP.conditions, XP.names, pathout)
batch.effects.pca.res

#
## Metagene
#

metagene.res <- metagene.all(XP.conditions, XP.names, pathout) 

##   Efficacy of monosome selection

metagene.monosome.res <- metagene.res[[1]]
metagene.monosome.res

##   Inflation of CDS-start codons coverage

metagene.inflation.res <- metagene.res[[2]]
metagene.inflation.res

##   Leakage of start and stop codons,

metagene.leakage.res <- metagene.res[[3]]
metagene.leakage.res

#
## Output Page in Html, readable in firefox, brave, chrome, safari or internet explorer.
#

outputQc(pathout, XP.conditions)

outputMine(pathout, XP.conditions)

carinelegrand/RiboVIEW documentation built on July 17, 2020, 3:02 p.m.