metagene.all: Monosome selection, START and STOP leakage, metagene

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

Description

metagene.all This function generates plots and indicative values for monosome selection, inflation around AUG codon and around STOP codon.

Usage

metagene.all(XP.conditions, XP.names, pathout, res1=0.1, res2=0.01)

Arguments

XP.conditions	Vector of experimental conditions for each sample
XP.names	Vector of names for each sample
pathout	Address where output files will be written
res1	Resolution of metagene
res2	Resolution of metagene around AUG and STOP

Value

This function returns 3 lists :

• Monosome selection (UTR reads)

  • plotAddress of plot file in png format

  • valueFraction of mRNAs where footprint cover only CDS and no UTRs (median and inter-quartile range)

  • colorColor white/orange/red corresponding to good/warning/poor level of quality

  • recommendationDescription and recommendation based on value

• Inflation of reads around AUG

  • plotAddress of plot file in png format

  • valueMedian ratio of coverage in 50 first codons in CDS / all CDS

  • colorColor white/orange/red corresponding to good/warning/poor level of quality

  • recommendationDescription and recommendation based on value

• Leakage at STOP codon

  • plotAddress of plot file in png format

  • valuelist of value$start : if any positive slope of metagene after AUG, p-value for this slope ; and value$stop : Ratio of coverage in [1 ; 1.3] just after STOP, as compared to [0.9 ; 1], just before STOP codon (median and standard deviation)

  • colorColor white/orange/red corresponding to good/warning/poor level of quality

  • recommendationDescription and recommendation based on value

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)

#
## 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

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