Q.make {QTLEMM}

Generate Q Matrix

Description

Generate the conditional probability matrix using the information of QTL and marker, along with the genotype data.

Usage

Q.make(
  QTL,
  marker,
  geno = NULL,
  interval = FALSE,
  type = "RI",
  ng = 2,
  cM = TRUE
)

Arguments

QTL

matrix. A q*2 matrix contains the QTL information, where the row dimension 'q' represents the number of QTLs in the chromosomes. The first column labels the chromosomes where the QTLs are located, and the second column labels the positions of QTLs (in morgan (M) or centimorgan (cM)).

marker

matrix. A k*2 matrix contains the marker information, where the row dimension 'k' represents the number of markers in the chromosomes. The first column labels the chromosomes where the markers are located, and the second column labels the positions of markers (in morgan (M) or centimorgan (cM)). It's important to note that chromosomes and positions must be sorted in order.

geno

matrix. A n*k matrix contains the genotypes of k markers for n individuals. The marker genotypes of P1 homozygote (MM), heterozygote (Mm), and P2 homozygote (mm) are coded as 2, 1, and 0, respectively, with NA indicating missing values.

interval

logical. When set to interval=TRUE, if a QTL shares the same position as a marker, the marker will be skipped and not considered as a flanking marker.

type

character. The population type of the dataset. Includes backcross (type="BC"), advanced intercross population (type="AI"), and recombinant inbred population (type="RI"). The default value is "RI".

ng

integer. The generation number of the population type. For instance, in a BC1 population where type="BC", ng=1; in an AI F3 population where type="AI", ng=3.

cM

logical. Specify the unit of marker position. If cM=TRUE, it denotes centimorgan; if cM=FALSE, it denotes morgan.

Value

The output contains k conditional probability matrices for the k flanking marker pairs (the k Q-matrices) and a conditional probability matrix of each QTL for all individuals (the cp-matrix) provided the genotype data of the testing population is input..

Note

If geno=NULL, the function can still be executed, and the output will contain k Q-matrices but no cp-matrix.

References

KAO, C.-H. and Z.-B. ZENG 1997 General formulas for obtaining the maximum likelihood estimates and the asymptotic variance-covariance matrix in QTL mapping when using the EM algorithm. Biometrics 53, 653-665. <doi: 10.2307/2533965.>

KAO, C.-H., Z.-B. ZENG and R. D. TEASDALE 1999 Multiple interval mapping for Quantitative Trait Loci. Genetics 152: 1203-1216. <doi: 10.1093/genetics/152.3.1203>

Examples

# load the example data
load(system.file("extdata", "exampledata.RDATA", package = "QTLEMM"))

# run and result
result <- Q.make(QTL, marker, geno)
head(result$cp.matrix)