cash-print: BC, FS and IC method: Print summary information

In tpbilton/GUSMap: Genotyping Uncertainty with Sequencing Data and Linkage Mapping (GUSMap)

BC, FS and IC method: Print summary information

Description

Method for printing summary information of an BC, FS or IC object

Usage

BCobj$print(what = NULL, ...)
FSobj$print(what = NULL, ...)
ICobj$print(what = NULL, ...)

Arguments

what	Character vector giving the type of information to be printed. IF NULL, then all the information is printed.

Details

There are four types of information availabe to be printed for an object (as specified by the what argument).

BC object:

"data"

Summary information of the data as process by the makeBC function.

"LG-pts"

Summary information of the pesudo-testcross linkage groups produced by the $createLG function.

"LG-bi"

Summary information of the combined linkage groups produced by either the $addBIsnps or $orderLG functions.

"map"

Summary information of the linkage maps produced by the $computeMap function.

FS object:

"data"

Summary information of the data as process by the makeFS function.

"LG-pts"

Summary information of the pesudo-testcross linkage groups produced by the $createLG function.

"LG-comb"

Summary information of the combined linkage groups produced by the $addBIsnps function.

"map"

Summary information of the linkage maps produced by the $computeMap function.

IC object:

"data"

Summary information of the data as process by the makeFS function.

"LG"

Summary information of the pesudo-testcross linkage groups produced by the $createLG function.

"map"

Summary information of the linkage maps produced by the $computeMap function.

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC

Examples

## simulate some sequencing data
set.seed(6745)
config <- list(replicate(2,sample(c(1,2,4), size=30, replace=TRUE), simplify=FALSE))
F1data <- simFS(0.01, config=config, meanDepth=10, nInd=50)
# print summary information of data
F1data$print(what = "data")

## Compute 2-point recombination fractions
F1data$rf_2pt()
## create paternal and maternal linkage groups
F1data$createLG()
## Add BI SNPs
F1data$addBIsnps()

# print information of the combined linkage groups
F1data$print(what = "LG-comb")
#print both the data infromation and separate linkage groups
F1data$print(what = c("data", "LG-pts"))

tpbilton/GUSMap documentation built on Feb. 22, 2025, 12:27 p.m.