BC: BC object

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

BC object

Description

Class for storing BC data and associated functions for analysis of backcross family populations.

Usage

## Create BC object
BCobj <- makeBC(RAobj, pedfile, family=NULL, inferSNPs=FALSE,
                filter=list(MAF=0.05, MISS=0.2, BIN=100, DEPTH=5, PVALUE=0.01, MAXDEPTH=500))

## Functions (Methods) of an BC object
BCobj$addBIsnps(LODthres = 10, nComp = 10)
BCobj$iaddSNPs(LODthres = 10, nComp = 10)
BCobj$computeMap(chrom = NULL, init_r = 0.01, ep = 0.001, method = NULL, err = T, mapped = T, nThreads = 1, rfthres = 0.1)
BCobj$createLG(parent = "both", LODthres = 10, nComp = 10, reset = FALSE)
BCobj$maskSNP(snps)
BCobj$mergeLG(LG, where = NULL, mergeTo = NULL)
BCobj$orderLG(chrom = NULL, mapfun = "haldane", weight = "LOD2", ndim = 30, spar = NULL)
BCobj$plotChr(parent = "maternal", mat = "rf", filename = NULL, chrS = 2, lmai = 0.25)
BCobj$plotLG(parent  = "both", LG = NULL, mat = "rf", filename = NULL, interactive = FALSE, what = NULL)
BCobj$plotLM(LG = NULL, fun = "haldane", col = "black")
BCobj$plotSyn()
BCobj$print(what = NULL, ...)
BCobj$removeLG(LG, where = NULL)
BCobj$removeSNP(snps, where = NULL)
BCobj$rf_2pt(nClust = 2, err = FALSE)
BCobj$unmaskSNP(snps)
BCobj$writeLM(file, direct = "./", LG = NULL, what = NULL, inferGeno = TRUE)

Details

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

Methods(Functions)

$addBIsnps

Add Both-Informative (BI) snps to the maternal and/or paternal linkage groups.

$addSNPs

Add MI, PI and/or SI SNPs to the existing linkage groups

$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 BC 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 -> BC

Methods

Public methods

• BC$new()

• BC$print()

• BC$removeSNP()

• BC$removeLG()

• BC$mergeLG()

• BC$maskSNP()

• BC$unmaskSNP()

• BC$rf_2pt()

• BC$createLG()

• BC$addSNPs()

• BC$addBIsnps()

• BC$orderLG()

• BC$plotLG()

• BC$plotChr()

• BC$plotLM()

• BC$plotSyn()

• BC$computeMap()

• BC$cometPlot()

• BC$rocketPlot()

• BC$RDDPlot()

• BC$writeLM()

• BC$clone()

Inherited methods

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

---

Method new()

Usage

BC$new(R6obj)

---

Method print()

Usage

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

---

Method removeSNP()

Usage

BC$removeSNP(snps, where = NULL)

---

Method removeLG()

Usage

BC$removeLG(LG, where = NULL)

---

Method mergeLG()

Usage

BC$mergeLG(LG, where = NULL, mergeTo = NULL)

---

Method maskSNP()

Usage

BC$maskSNP(snps)

---

Method unmaskSNP()

Usage

BC$unmaskSNP(snps)

---

Method rf_2pt()

Usage

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

---

Method createLG()

Usage

BC$createLG(parent = "both", LODthres = 10, nComp = 10, reset = FALSE)

---

Method addSNPs()

Usage

BC$addSNPs(LODthres = 10, nComp = 10)

---

Method addBIsnps()

Usage

BC$addBIsnps(LODthres = 10, nComp = 10)

---

Method orderLG()

Usage

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

---

Method plotLG()

Usage

BC$plotLG(
  parent = "both",
  LG = NULL,
  mat = "rf",
  filename = NULL,
  interactive = FALSE,
  what = NULL,
  ...
)

---

Method plotChr()

Usage

BC$plotChr(
  chrom = NULL,
  parent = "maternal",
  mat = c("rf"),
  filename = NULL,
  chrS = 2,
  lmai = 0.25
)

---

Method plotLM()

Usage

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

---

Method plotSyn()

Usage

BC$plotSyn()

---

Method computeMap()

Usage

BC$computeMap(
  parent = "both",
  chrom = NULL,
  init_r = 0.001,
  ep = 0.001,
  method = NULL,
  err = TRUE,
  multiErr = FALSE,
  mapped = TRUE,
  nThreads = 1,
  inferOPGP = TRUE,
  rfthres = 0.1
)

---

Method cometPlot()

Usage

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

---

Method rocketPlot()

Usage

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

---

Method RDDPlot()

Usage

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

---

Method writeLM()

Usage

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

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BC$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.