outputQc: Web output to visualize quality control diagnostics in...

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

Description

outputQc This function takes a list of sample conditions as input and generates a web page for visualisation of quality control diagnostics.

Usage

outputQc(pathout, XP.conditions)

Arguments

pathout	Address where output files will be written
XP.conditions	Vector of experimental conditions for each sample

Details

This function loads all plots, values and text descriptions generated by Riboview functions and generates an html page containing all this information organized by categories, and by tabs in each category.

Value

The file "Results-Qc.html", readable in a suitable internet browser, is written to pathout. Compatible browsers are up-to-date version of firefox, safari and IE.

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.