mcalls2mkobj: mcalls2mkobj() This function will select BWASP mcalls files...

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

Description

mcalls2mkobj() This function will select BWASP mcalls files according to specified selection criteria and read the data into methylBase objects.

Usage

mcalls2mkobj(
  inputdf,
  species = "all",
  study = "all",
  sample = "all",
  replicate = c(1:20),
  type = "CpGhsm",
  mincov = 1,
  assembly = "unknown"
)

Arguments

inputdf	A data frame as returned by setup_BWASPR from the input data file. Each row corresponds to a BWASP-generated output, with columns indicating Species, Study, Sample, Replicate, Type, and File.
species	A character string specifying the Species to be pulled out of inputdf; default: "all".
study	A list of character strings specifying the Studies to be pulled out of inputdf; default: "all".
sample	A list of character strings specifying the Samples to be pulled out of inputdf; default: "all".
replicate	A list of integers specifying the Replicates to be pulled out of inputdf; default: c(1:20).
type	The type should be CpGhsm or CpGscd, as per BWASP output.
mincov	Integer value specifying the mincov parameter for readMeth(); default: 1.
assembly	Label for the underlying genome assembly version; default: "unknown".

Value

A methylKit-package methylRaw or methylRawList object (NULL if no matching data are found).

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",type="CpGhsm",
               mincov=1,assembly="Amel-4.5")

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