periodicity: Functions related to periodicity around AUG (periodicity and...

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

Description

periodicity This function takes a list of bam files as input and annotations in input, generate coverage counts around AUG and produces recurrence and periodicity plots.

Usage

periodicity(list.bam, refCDS, refFASTA, pathout, 
         XP.names, versionStrip = FALSE, 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
pathout	Address where output files will be written
XP.names	Vector of names for each sample
versionStrip	Indicates if version number should be trimmed, for example NM_001276351.1 would be trimmed to NM_001276351 (defaults to FALSE)
python.messages	Print or not messages from Python script calls (defaults to TRUE)

Details

This function calls the Python script periodicity.py to generate coverage counts around AUG, and generates periodicity recurrence plot and periodicity barplot based on these counts.

Value

The following files are written to pathout :

OL-*.txt

Coverage around AUG for each sample

OL-*_recurr.png

Periodicity recurrence plot for each sample

OL-*_period.png

Periodicity barplot for each sample

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)

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