stringCoverage.control {STRMPS}

String coverage coontrol object

Description

String coverage coontrol object

Usage

stringCoverage.control(motifLength = 4, Type = "AUTOSOMAL",
  simpleReturn = TRUE, includeLUS = FALSE, numberOfThreads = 4L,
  meanFunction = mean, includeAverageBaseQuality = FALSE, trace = FALSE,
  uniquelyAssigned = TRUE)

Arguments

motifLength

The motif lengths of each marker.

Type

The chromosome type of each marker (autosomal, X, or Y).

simpleReturn

TRUE/FALSE: Should the returned object be simplified?

includeLUS

TRUE/FALSE: Should the LUS of each region be calculated?

numberOfThreads

The number of cores used for parallelisation.

meanFunction

The function used to average the base qualities.

includeAverageBaseQuality

Should the average base quality of the region be included?

trace

TRUE/FALSE: Show trace?

uniquelyAssigned

TRUE/FALSE: Should regions not uniquely assigned be removed?

Details

Control function for the 'stringCoverage' function. Sets default values for the parameters.

Value

List of parameters used for the 'stringCoverage' function.