demo/README.md

In BrendelGroup/BWASPR: Various R functions and scripts for the analyis of BWASP workflow output

BWASPR Demo

Analyses in this directory are based on the BWASPR package, available on github:

https://github.com/brendelgroup/BWASPR

As documented on the github page, BWASPR processes (BWASP-generated) .mcalls files. Input specification is via two files: the .dat data file and the *.par parameter file, which are read by the BWASPR function setup_BWASPR().

Although there are of course several ways of running R-based workflows, the data studies in this directory were conveniently produced by Rscript. The workflow is represented in the file

Rscript.BWASPR

which coulde be invoked as follows (putting output into OUT-arg1):

Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats  Rscript.BWASPR arg1 OUT-arg1

where arg1 is the prefix of a configuration file arg1.conf. The command will source(arg1.conf) within Rscript.BWASPR, then run the workflow according to the specifications in arg1.conf.

For convenience and testing, use

./xcheck arg1

which will call the Rscript command and put output in a directory NEW-arg1 (and compare with an existing output directory OUT-arg1, if it exists, a useful check on updated code).

What will be run is determined by the logicals RUNsomething in the *.conf file. The default

RUNload    <- FALSE

RUNcms     <- TRUE
RUNpwc     <- TRUE
RUNcrl     <- TRUE

RUNrepcms  <- TRUE
RUNrepcrl  <- TRUE

RUNmmp     <- TRUE
RUNacs     <- TRUE
RUNrnk     <- TRUE
RUNmrpr    <- TRUE

RUNdmt     <- TRUE
RUNdmsg    <- TRUE
RUNdmgdtls <- TRUE
RUNogl     <- TRUE

RUNsave    <- FALSE

would run all implemented analyses from scratch. To omit certain steps (e.g., to re-run only some of the analyses with changed parameters), change TRUE to FALSE. RUNload=TRUE will load a previously saved arg1.RData file into the R workspace before executing other analyses steps. To generate an arg1.RData file from the current run, set RUNsave=TRUE.

To check the mechanics of running BWASPR, you can use the small data set in ../inst/exdata. Run

./xdoit sample OUT-sample

and take a look at the 0README files in the output directory and its subdirectories.

If you decided to forgo the R package installation on your machine but have Singularity installed, then the following will do nicely:

singularity pull --name bwaspr.simg shub://BrendelGroup/BWASPR
singularity exec -e -B `pwd` bwaspr.simg ./xcheck sample

(using xcheck here in case you ran xdoit and want to compare local versus singularity output).

From sample to real data:

This demo is designed to show you the mechanics of the workflow on a small data set. So, how do you get a real data set? Back to BWASP, which tells you how to generate the required *.mcalls and GFF3DIR files.

BrendelGroup/BWASPR documentation built on Feb. 6, 2022, 9:09 a.m.