cALD {pould}

Calculation of the D', Wn, and conditional Asymmetric LD Measures

Description

Calculates D', Wn (Cramer's V) and Thomson and Single's conditional asymmetric LD (ALD) measures for pairs of loci.

Usage

cALD(
  dataSet,
  inPhase = FALSE,
  verbose = TRUE,
  saveVector = FALSE,
  vectorName = "",
  vectorPrefix = "",
  vecDir = tempdir()
)

Arguments

dataSet

A data frame or tab delimited file consisting of four columns of genotype data named, e.g. locus1_1 locus1_2 locus2_1 locus2_2, with 1 row per sample. The columns must be organized in this exact order, but the column names should not have _1 or _2 appended; use the same locus name for each column of a given locus. For phased data, locus1_1 is in phase with locus2_1, and locus1_2 is in phase with locus_2_2. Because this funciton operates on locus pairs, any rows with missing data should be excluded from the input genotype data.

inPhase

A boolean identifying the genotyping data as phased or unphased (TRUE = phased; FALSE = unphased); default is unphased.

verbose

A boolean identifying if results should be printed to the console (verbose = TRUE), or returned in a vector of (D', Wn, WLocus2/Locus1, WLocus1/Locus2, number of haplotypes) (verbose = FALSE)

saveVector

A boolean identifying if the vector of all haplotypes should be exported as a text file (saveVector = TRUE), or not (saveVector = FALSE).

vectorName

A name for the exported haplotype vector file; this name is not used if saveVector = FALSE. If a name is unspecified, then a filename including the locus-pair and a timestamp is generated.

vectorPrefix

An optional prefix for the haplotpe vector to be used if saveVector = TRUE. This prefix will be appended, along with the phase status, before the locus name and timestamp. LDWrap() uses this parameter to identify the dataset and haplotype information passed to cALD().

vecDir

The directory into which the haplotype vector should be written if saveVector = TRUE. The default is the directory specified by tempdir().

Details

LD results can be directed to the console or to a data file or data frame object. This function can generate a haplotype vector file for each locus pair analyzed, and will return the LD results eiher in the console, or as a data frame object. The implementation of ALD applied here is calculated using individual Dij LD values and allele frequencies.

Value

A vector of D', Wn, WLocus2/Locus1, WLocus1/Locus2 values, and the number of haplotypes evaluated

References

Thomson G. & Single R.M. GENETICS 2014;198(1):321-31. https://doi.org/10.1534/genetics.114.165266

Examples

# Analyze the first 10 rows of the included drb1.dqb1.demo genotype dataset
# and report LD results to the console.
cALD(drb1.dqb1.demo[1:10,])
# Alternatively, return a vector of LD results.
LDvec <- cALD(drb1.dqb1.demo[1:10,],verbose=FALSE)