repl.correl.codon: Correlation of footprint coverage at codon resolution

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

Description

repl.correl.codon This function takes a list of samples and experimental conditions in input, calculates correlations at codon level between replicates.

Usage

repl.correl.codon(list.bam, refCDS, refFASTA, mini, maxi, 
                    XP.names, XP.conditions, pathout)

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

Value

This function returns a list containing the following :

cor

Correlation between replicates

plot

Address of plot file in png format

value

Median of correlation across different conditions

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)

#
## 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

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