FS: FS object

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

FS object

Description

Class for storing RA data and associated functions for analysis of full-sib family populations.

Usage

## Create FS object
FSobj <- makeFS(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 FS object
FSobj$addBIsnps(LODthres = 10, nComp = 10)
FSobj$addSNPs(LODthres = 10, nComp = 10)
FSobj$computeMap(chrom = NULL, init_r = 0.01, ep = 0.001, method = "optim", sexSpec = F, err = T, mapped = T, nThreads = 1)
FSobj$createLG(parent = "both", LODthres = 10, nComp = 10)
FSobj$maskSNP(snps)
FSobj$mergeLG(LG, where = NULL, mergeTo = NULL)
FSobj$orderLG(chrom = NULL, mapfun = "haldane", weight = "LOD2", ndim = 30, spar = NULL)
FSobj$plotChr(parent = "maternal", mat = "rf", filename = NULL, chrS = 2, lmai = 2)
FSobj$plotLG(parent = "maternal", LG = NULL, mat = "rf", filename = NULL, interactive = TRUE, what = NULL)
FSobj$plotLM(LG = NULL, fun = "haldane", col = "black")
FSobj$plotSyn()
FSobj$print(what = NULL, ...)
FSobj$removeLG(LG, where = NULL)
FSobj$removeSNP(snps, where = NULL)
FSobj$rf_2pt(nClust = 2, err = FALSE)
FSobj$unmaskSNP(snps)
FSobj$writeLM(file, direct = "./", LG = NULL, what = NULL, inferGeno=TRUE)

Details

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

Methods(Functions)

$addBIsnps

Add Both-Informative (BI) snps to the maternal and/or paternal linkage groups and merge the parental 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 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 -> FS

Methods

Public methods

• FS$new()

• FS$print()

• FS$removeSNP()

• FS$removeLG()

• FS$mergeLG()

• FS$maskSNP()

• FS$unmaskSNP()

• FS$rf_2pt()

• FS$createLG()

• FS$addSNPs()

• FS$addBIsnps()

• FS$orderLG()

• FS$plotLG()

• FS$plotChr()

• FS$plotLM()

• FS$plotSyn()

• FS$computeMap()

• FS$writeLM()

• FS$cometPlot()

• FS$rocketPlot()

• FS$RDDPlot()

• FS$clone()

Inherited methods

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

---

Method new()

Usage

FS$new(R6obj)

---

Method print()

Usage

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

---

Method removeSNP()

Usage

FS$removeSNP(snps, where = NULL)

---

Method removeLG()

Usage

FS$removeLG(LG, where = NULL)

---

Method mergeLG()

Usage

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

---

Method maskSNP()

Usage

FS$maskSNP(snps)

---

Method unmaskSNP()

Usage

FS$unmaskSNP(snps)

---

Method rf_2pt()

Usage

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

---

Method createLG()

Usage

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

---

Method addSNPs()

Usage

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

---

Method addBIsnps()

Usage

FS$addBIsnps(LODthres = 10, nComp = 10, binsize = 0)

---

Method orderLG()

Usage

FS$orderLG(
  LG = NULL,
  mapfun = "haldane",
  weight = "LOD2",
  binsize = 0,
  ndim = 30,
  spar = NULL,
  filename = NULL
)

---

Method plotLG()

Usage

FS$plotLG(
  parent = "maternal",
  LG = NULL,
  mat = "rf",
  filename = NULL,
  interactive = TRUE,
  what = NULL,
  ...
)

---

Method plotChr()

Usage

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

---

Method plotLM()

Usage

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

---

Method plotSyn()

Usage

FS$plotSyn()

---

Method computeMap()

Usage

FS$computeMap(
  chrom = NULL,
  init_r = 0.001,
  ep = 0.001,
  method = NULL,
  sexSpec = FALSE,
  err = TRUE,
  multiErr = FALSE,
  mapped = TRUE,
  nThreads = 1,
  inferOPGP = TRUE,
  rfthres = 0.1
)

---

Method writeLM()

Usage

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

---

Method cometPlot()

Usage

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

---

Method rocketPlot()

Usage

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

---

Method RDDPlot()

Usage

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

---

Method clone()

The objects of this class are cloneable with this method.

Usage

FS$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.