| gl.infer.sex {dartR.sexlinked} | R Documentation |
Uses sex-linked loci to infer sex of individuals
Description
This function uses the output of function gl.keep.sexlinked (list of 5 elements) to infer the sex of all individuals in the dataset. It uses 3 types of sex-linked loci (W-/Y-linked, Z-/X-linked, and gametologs), assigns a preliminary genetic sex for each type of sex-linked loci available, and outputs an agreed sex.
This function produces as output a dataframe with individuals in rows and 11 columns.
Usage
gl.infer.sex(gl_sexlinked, system = NULL, seed = NULL)
Arguments
gl_sexlinked |
The output of function gl.keep.sexlinked (complete list with 5 elements). See explanation in "Details" section [required]. |
system |
String that declares the sex-determination system of the species: 'zw' or 'xy' [required]. |
seed |
User-defined integer for repeatability purposes. If not provided by user, it is chosen randomly by default. See "Details" section. |
Details
Parameter gl_sexlinked must be the name of the output object (a
list of 5 elements) produced by function gl.keep.sexlinked. Parameter
seed must be an integer that will be used on the KMeans algorithm used
by the function. We highly recommend choosing the seed to guarantee
repeatability.
Note that this function was created with the explicit intent that a human checks the evidence for the sex assignments that do NOT agree for all types of sex-linked loci (called "indefinite sex assignments" and denoted as "*M" or "*F" in the last column of dataframe output). This human can then use their criterion to validate these assignments.
Function's output
This function creates a dataframe with one row per individual and 11 columns:
-
id > Individuals' ID.
-
w.linked.sex or y.linked.sex > Sex inferred using w-linked or y-linked loci.
-
#called > Number of W-linked or Y-linked loci for which the individual had a called genotype (cf. missing genotype).
-
#missing > Number of W-linked or Y-linked loci for which the individual had a missing genotype (cf. called genotype).
-
z.linked.sex or x.linked.sex > Sex inferred using z-linked or x-linked loci.
-
#Hom.z or #Hom.x > Number of z-linked or x-linked loci for which the individual is homozygous.
-
#Het.z or #Het.x > Number of z-linked or x-linked loci for which the individual is heterozygous.
-
gametolog.sex > Sex inferred using gametologs.
-
#Hom.g > Number of gametologous loci for which the individual is homozygous.
-
#Het.g > Number of gametologous loci for which the individual is heterozygous.
-
agreed.sex > Agreed sex: 'F' or 'M' if all preliminary sex-assignments match (i.e., definite sex assignment), and '*F' or '*M' if NOT all preliminary sex-assignments match (i.e., indefinite sex assignment).
Value
A dataframe.
Author(s)
Custodian: Diana Robledo-Ruiz – Post to https://groups.google.com/d/forum/dartr
References
Robledo‐Ruiz, D. A., Austin, L., Amos, J. N., Castrejón‐Figueroa, J., Harley, D. K., Magrath, M. J., Sunnucks, P., & Pavlova, A. (2023). Easy‐to‐use R functions to separate reduced‐representation genomic datasets into sex‐linked and autosomal loci, and conduct sex assignment. Molecular Ecology Resources, 00, 1-21.
Examples
LBP_sexLinked <- gl.keep.sexlinked(x = LBP, system = "xy", plot.display = TRUE, ncores = 1)
inferred.sexes <- gl.infer.sex(gl_sexlinked = LBP_sexLinked, system = "xy", seed = 100)
inferred.sexes