chx.artefacts: Artefacts visible on codon enrichment, due to cycloheximide...

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

Description

chx.artefacts This function takes a list of samples and their conditions as input and visualizes enrichment around AUG +/- 90 codons, where possible artefacts due to drugs used in the experiment should be visible.

Usage

chx.artefacts(XP.conditions, XP.names, pathout, algo="unbiased")

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
algo	Algorithm used, either "unbiased" (default) or "Hussmann"

Details

This function plots enrichment of codons around AUG and 2 further plots dedicated to Arginine codons or to Lys-aaa codon.

Value

This function returns a list containing the following :

plot

Address of png plot file

value

Standard deviation of enrichment for each codon

color

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

recommendation

Description 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)

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

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

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