enrichmentNoccupancy: Calculates unbiased codon enrichment, Hussmann's codon...

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

Description

enrichmentNoccupancy 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

enrichmentNoccupancy(list.bam, refCDS, refFASTA, mini, maxi, XP.names,  
                     pathout, versionStrip = FALSE, r.messages=TRUE, python.messages=TRUE)

Arguments

list.bam	List of bam files containing aligned reads for each sample (same order as in XP.names)
refCDS	Address of file containing coding sequence annotation. This file should contain tab-separated values for mRNA name, nt position of start codon, nt position of first codon after stop codon, for example : ID localStart localEnd NM_001276351 145 1348 NM_001276352 145 799 NM_000299 251 2495
refFASTA	Address of reference sequences for mRNA of the studied organism
mini	Minimum footprint length to consider (as selected by user)
maxi	Maximum footprint length to consider (as selected by user)
XP.names	Vector of names for each sample
pathout	Address where output files will be written
versionStrip	Indicates if version number should be trimmed, for example NM_001276351.1 would be trimmed to NM_001276351 (defaults to FALSE)
r.messages	Print or not interactive messages from R (defaults to TRUE)
python.messages	Print or not messages from Python script calls (defaults to TRUE)

Details

This function relies on python script enrichment.py. Where possible, calculations are run in parallel. The user should confirm or tailor the selected number of cores to use for the parallel computations. Codon enrichment and bulk occupancy are defined in Legrand et al. 2019 (TBC)

Value

Output files ar written directly to pathout. These files are :

BCO-*.txt.codonEnrichment_mean

Mean codon enrichment (unbiased)

BCO-*.txt.codonEnrichment_sd

Standard deviation of codon enrichment

BCO-*.txt.codonCover_mean

Mean codon enrichment (Hussmann)

BCO-*.txt.codonCover_sd

Standard deviation of Hussmann's codon enrichment

BCO-*.txt

Bulk Codon Occupancy

BCO-*.txt.limCod

Codon counts at footprint limits

BCO-*.txt.limNt

Nucleotide counts at footprint limits

BCO-*.txt.nbreads

Nb of reads per mRNA

BCO-*.txt.SCO

Coverage for A site per mRNA and position, and single codon occupancy

BCO-*.txt.metagene

Coverage for A site per mRNA and metagene position Note that this contains also UTRs and regions close to AUG or STOP codons, contrary to other output files.

BCO-*.txt.paused

List of paused sites with their sequence context

BCO-*.txt.RPKM

Number of reads per kilo base per million mapped reads, for each mRNA.

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)
 

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