IC: IC object

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

IC object

Description

Class for storing RA data and associated functions for analysis of intercross (F2) populations.

Usage

## Create IC object
ICobj <- makeIC(RAobj, samID=NULL,
                filter=list(MAF=0.05, MISS=0.2, BIN=100, DEPTH=5, PVALUE=0.01, MAXDEPTH=500))

## Functions (Methods) of an IC object
ICobj$computeMap(chrom = NULL, init_r = 0.01, ep = 0.001, method = "EM", err = T, mapped = T, nThreads = 1)
ICobj$createLG(LODthres = 10, nComp = 10)
ICobj$maskSNP(snps)
ICobj$mergeLG(LG)
ICobj$orderLG(chrom = NULL, mapfun = "haldane", weight = "LOD2", ndim = 30, spar = NULL)
ICobj$plotChr(mat = "rf", filename = NULL, chrS = 2, lmai = 2)
ICobj$plotLG(LG = NULL, mat = "rf", filename = NULL, interactive = TRUE)
ICobj$plotLM(LG = NULL, fun = "haldane", col = "black")
ICobj$plotSyn()
ICobj$print(what = NULL, ...)
ICobj$removeLG(LG)
ICobj$removeSNP(snps)
ICobj$rf_2pt(nClust = 2, err=FALSE)
ICobj$unmaskSNP(snps)
ICobj$writeLM(file, direct = "./", LG = NULL, what = NULL, inferGeno = TRUE)

Details

An IC object is created from the makeIC function and contains RA data, various statistics of the dataset that have been computed, and functions (methods) for analyzing the data. Information in an IC object are specific to intercross (F2) populations.

Methods(Functions)

$createLG

Create linkage group(s).

$computeMap

Compute linkage maps for a given marker order.

$maskSNP

Mask SNP(s) in the dataset.

$mergeLG

Merge linkage groups.

$orderLG

Order the SNPs in the linkage group(s).

$plotChr

Plot the heatmap of the 2-point recombination fraction estimates (or LOD scores) when SNPs are ordered according to the genome assembly.

$plotLG

Plot the heatmap of the 2-point recombination fraction estimates (or LOD scores) when SNPs are ordered according to their linkage groups.

$plotLM

Plot linkage maps.

$plotSyn

Produce a Synteny plot.

$print

Print summary information for FS object.

$removeLG

Remove linkage group(s).

$removeSNP

Remove SNP(s) from linkage group(s).

$rf_2pt

Compute the 2-point recombination fraction (and LOD score) between all SNP pairs.

$unmaskSNP

Unmask SNP(s) in the data set.

$writeLM

Write linkage mapping results to a file.

Super class

GUSbase::RA -> IC

Methods

Public methods

• IC$new()

• IC$print()

• IC$removeSNP()

• IC$removeLG()

• IC$mergeLG()

• IC$maskSNP()

• IC$unmaskSNP()

• IC$rf_2pt()

• IC$createLG()

• IC$orderLG()

• IC$plotLG()

• IC$plotChr()

• IC$plotLM()

• IC$plotSyn()

• IC$computeMap()

• IC$writeLM()

• IC$cometPlot()

• IC$rocketPlot()

• IC$RDDPlot()

• IC$clone()

Inherited methods

• GUSbase::RA$extractVar()
• GUSbase::RA$mergeSamples()
• GUSbase::RA$writeRA()
• GUSbase::RA$writeVCF()

---

Method new()

Usage

IC$new(R6obj)

---

Method print()

Usage

IC$print(what = NULL, ...)

---

Method removeSNP()

Usage

IC$removeSNP(snps)

---

Method removeLG()

Usage

IC$removeLG(LG)

---

Method mergeLG()

Usage

IC$mergeLG(LG)

---

Method maskSNP()

Usage

IC$maskSNP(snps)

---

Method unmaskSNP()

Usage

IC$unmaskSNP(snps)

---

Method rf_2pt()

Usage

IC$rf_2pt(nClust = 2, err = FALSE)

---

Method createLG()

Usage

IC$createLG(LODthres = 10, nComp = 10, reset = FALSE)

---

Method orderLG()

Usage

IC$orderLG(
  LG = NULL,
  mapfun = "haldane",
  weight = "LOD2",
  ndim = 30,
  spar = NULL,
  filename = NULL
)

---

Method plotLG()

Usage

IC$plotLG(LG = NULL, mat = "rf", filename = NULL, interactive = TRUE, ...)

---

Method plotChr()

Usage

IC$plotChr(chrom = NULL, mat = c("rf"), filename = NULL, chrS = 2, lmai = 2)

---

Method plotLM()

Usage

IC$plotLM(LG = NULL, fun = "haldane", col = "black")

---

Method plotSyn()

Usage

IC$plotSyn()

---

Method computeMap()

Usage

IC$computeMap(
  chrom = NULL,
  init_r = 0.001,
  ep = 0.001,
  method = "EM",
  err = TRUE,
  multiErr = FALSE,
  mapped = TRUE,
  nThreads = 1,
  inferOPGP = TRUE,
  rfthres = 0.1,
  ...
)

---

Method writeLM()

Usage

IC$writeLM(file, direct = "./", LG = NULL, what = NULL, inferGeno = TRUE)

---

Method cometPlot()

Usage

IC$cometPlot(
  filename = NULL,
  cex = 1,
  maxdepth = 500,
  maxSNPs = 1e+05,
  res = 300,
  color = NULL,
  ind = FALSE,
  ncores = 1,
  ...
)

---

Method rocketPlot()

Usage

IC$rocketPlot(
  ploid = 2,
  filename = NULL,
  cex = 1,
  maxdepth = 500,
  maxSNPs = 1e+05,
  res = 300,
  scaled = TRUE,
  ...
)

---

Method RDDPlot()

Usage

IC$RDDPlot(filename = NULL, maxdepth = 500, maxSNPs = 1e+05, ...)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

IC$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Author(s)

Timothy P. Bilton

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