Description Usage Arguments Details Value Author(s) References
View source: R/diveRsity-code.R
This function calculates locus and pairwise confidence intervals for Weir & Cockerham's (1984) F_ST and F_IT. These statistics can also be calculated using the divPart
function, however, fstOnly
is designed to be more memory efficient for larger datasets (e.g. SNPs).
1 2 |
infile |
Specifying the name of the ‘genepop’ (Rousset, 2008) file from which the statistics are to be calculated This file can be in either the 3 digit of 2 digit format, and must contain only one whitespace separator (e.g. “space” or “tab”) between each column including the individual names column. The number of columns must be equal to the number of loci + 1 (the individual names column). If this file is not in the |
outfile |
Allows users to specify a prefix for an output folder. Name must a character string enclosed in either “” or ''. |
gp |
Specifies the digit format of the |
bs_locus |
Specifies whether locus bootstrapped confidence intervals should be calculated. |
bs_pairwise |
Specified whether pairwise population bootstrapped confidence intervals should be calculated. |
bootstraps |
Determines the number of bootstrap iterations to be carried out. The default value is |
parallel |
A logical input, indicating whether your analysis should be run in parallel mode or sequentially. |
Because fstOnly
is intended to maximise memory (RAM) efficiency, the funciton does not provide many of the plotting utilities that divPart
does.
locus |
A list object containing two matrices, F_ST and F_IT. These matrices contain actual, lower 95% confidence interval and upper 95% confidence interval per locus. Global values are also presented with their respective confidence intervals. |
pairwise |
A list object containing two matrices, F_ST and F_IT. These matrices contain actual, lower 95% confidence interval and upper 95% confidence interval per pairwise population comparison. |
Kevin Keenan <kkeenan02@qub.ac.uk>
Rousset, F., “genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,” Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).
Weir, B.S. & Cockerham, C.C., Estimating F-Statistics, for the Analysis of Population Structure, Evolution, vol. 38, No. 6, pp. 1358-1370 (1984).
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