CAnD: Peform the CAnD Test
In CAnD: Perform Chromosomal Ancestry Differences (CAnD) Analyses

Description Usage Arguments Value Author(s) References Examples

Perform the CAnD test on a set of ancestry proportions estimated for a particular ancestral subpopulation of interest

1	CAnD(chrAncest, bonfCorr = TRUE)

`chrAncest`	A data.frame holding the ancestral proportions; each row corresponds to a sample and each column corresponds to a chromosomal/chromosomal segment ancestry proportion. Note: only include the proportions for one ancestral population at a time.
`bonfCorr`	A logical argument indicating whether the p-value should be corrected for multiple testing using Bonferroni correction. The default is `TRUE`.

A CAnDResult object holding the p-value for each chromosome/chromosomal segment, the overall CAnD p-value, the CAnD statistic and whether the Bonferroni multiple testing correction was used.

Caitlin McHugh mchughc@uw.edu

McHugh, C., Brown, L., Thornton, T. Detecting heterogeneity in population structure across the genome in admixed populations. Genetics, 2016.

data(ancestries)
euroCols <- grep("Euro",colnames(ancestries))
euro <- ancestries[,euroCols]
res <- CAnD(euro)
res

CAnD results for parametric test
Bonferroni correction was used
p-values = 0.00971
 p-values = 7.16e-65
 p-values = 4.97e-07
 p-values = 8.59e-05
 p-values = 1.68e-07
 p-values = 0.000251
 p-values = 0.00421
 p-values = 0.00801
 p-values = 0.145
 p-values = 0.163
 p-values = 0.000133
 p-values = 0.336
 p-values = 1.88e-05
 p-values = 0.00491
 p-values = 0.000826
 p-values = 0.000624
 p-values = 0.011
 p-values = 1.05e-05
 p-values = 0.000151
 p-values = 0.00138
 p-values = 3.79e-07
 p-values = 0.0188
 p-values = 6.01e-55
observed CAnD statistic = 11300
calculated CAnD p-value = 0