ukb_gen_rel_count | R Documentation |
Creates a summary count table of the number of individuals and pairs at each degree of relatedness that occurs in the UKB sample, and an optional plot.
ukb_gen_rel_count(data, plot = FALSE)
data |
A dataframe of the genetic relatedness data including KING kinship coefficient, and proportion of alleles IBS = 0. See Details. |
plot |
Logical indicating whether to plot relatedness figure. Default = FALSE. |
Use UKB supplied program 'ukbgene' to retrieve genetic relatedness data file ukbA_rel_sP.txt. See UKB Resource 664. The count and plot include individuals with IBS0 >= 0.
If plot = FALSE
(default), a count of individuals and pairs
at each level of relatedness. If plot = TRUE
, reproduces the
scatterplot of genetic relatedness against proportion of SNPs shared IBS=0
(each point representing a pair of related UKB individuals) from the
genotyping and quality control
documentation.
ukb_gen_related_with_data
,
ukb_gen_samples_to_remove
## Not run: # Use UKB supplied program `ukbgene` to retrieve genetic relatedness file ukbA_rel_sP.txt. See \href{http://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=664}{UKB Resource 664}. With the whitespace delimited file read into R as e.g. ukb_relatedness, generate a dataframe of counts or a plot as follows: ukb_gen_rel_count(ukb_relatedness) ukb_gen_rel_count(ukb_relatedness, plot = TRUE) ## End(Not run)
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