setup_BWASPR: setup_BWASPR() Setting up a BWASPR analysis structure

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

Description

setup_BWASPR() Setting up a BWASPR analysis structure

Usage

setup_BWASPR(datafile, parfile)

Arguments

datafile	A BWASP data description file consisting of rows of tab-deliminted entries with consecutive labesl for Species, Study, Sample, Replicate, Type, and BWASP mcalls file location.
parfile	A BWASPR parameter file with parameter settings used in in the analysis.

Value

A list consisting of a data frame with the data input file paths (identified as list item "datafiles") and a data frame with parameter assignments (identified as list item "parameters")

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  myfiles$parameters[myfiles$parameters$Variable == "ASSEMBLYVERSION",2]
  as.numeric(myfiles$parameters[myfiles$parameters$Variable == "GENOMESIZE",2])

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