Multi-loci analysis

Before using this tutorial, we recommend that you read through our introductory tutorial.

DiffSegR can analyze multiple loci of interest, including across various chromosomes. To do so you can add one line per locus to the data.frame accepted as input by newExperiment() (see hereafter). Alternatively, the function also accepts a path to a tabular format file with similar columns (seqid, chromStart, chromEnd, locusID). The rest of the analysis can be conducted similarly to the analysis of a single locus.

data <- newExperiment(
  sampleInfo   = sample_info,
  loci         = data.frame(
    seqid      = c("ChrC", "Chr1"), 
    chromStart = c(71950, 2421089), 
    chromEnd   = c(78500, 2422066),
    locusID    = c("psbB_petD", "F24B9")
  ),
  referenceCondition = "wt",
  otherCondition     = "pnp1_1",
  nbThreads          = 4,
  nbThreadsByLocus   = 2,
  coverage           = working_directory
)

Note : Here, the total number of threads used for the analysis is 4, with 2 allocated per locus. Since the analysis involves two loci, at the appropriate time, both will be loaded into memory and processed simultaneously.