Description Usage Arguments Details Value Author(s) References Examples
Calculate relatedness measures F-statistics (also known as fixation indices) for given populations
1 2 3 |
gdsobj |
an object of class |
population |
a factor, indicating population information for each individual |
method |
|
sample.id |
a vector of sample id specifying selected samples; if NULL, all samples are used |
snp.id |
a vector of snp id specifying selected SNPs; if NULL, all SNPs are used |
autosome.only |
if |
remove.monosnp |
if TRUE, remove monomorphic SNPs |
maf |
to use the SNPs with ">= maf" only; if NaN, no MAF threshold |
missing.rate |
to use the SNPs with "<= missing.rate" only; if NaN, no missing threshold |
with.id |
if |
verbose |
if |
The minor allele frequency and missing rate for each SNP passed in
snp.id
are calculated over all the samples in sample.id
.
The "W&H02"
option implements the calculation in Buckleton et. al.
2016.
Return a list:
sample.id |
the sample ids used in the analysis |
snp.id |
the SNP ids used in the analysis |
Fst |
weighted Fst estimate |
MeanFst |
the average of Fst estimates across SNPs |
FstSNP |
a vector of Fst for each SNP |
Beta |
Beta matrix |
Xiuwen Zheng
Weir, BS. & Cockerham, CC. Estimating F-statistics for the analysis of population structure. (1984).
Weir, BS. & Hill, WG. Estimating F-statistics. Annual review of genetics 36, 721-50 (2002).
Population-specific FST values for forensic STR markers: A worldwide survey. Buckleton J, Curran J, Goudet J, Taylor D, Thiery A, Weir BS. Forensic Sci Int Genet. 2016 Jul;23:91-100. doi: 10.1016/j.fsigen.2016.03.004.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | # open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
group <- as.factor(read.gdsn(index.gdsn(
genofile, "sample.annot/pop.group")))
# Fst estimation
v <- snpgdsFst(genofile, population=group, method="W&C84")
v$Fst
v$MeanFst
summary(v$FstSNP)
# or
v <- snpgdsFst(genofile, population=group, method="W&H02")
v$Fst
v$MeanFst
v$Beta
summary(v$FstSNP)
# close the genotype file
snpgdsClose(genofile)
|
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
[1] 0.1443145
[1] 0.1245116
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-0.007271 0.043952 0.095479 0.124512 0.172969 0.791881 1
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
[1] 0.133837
[1] 0.1205067
CEU HCB JPT YRI
CEU 0.11405722 0.03754189 0.03604618 -0.08262898
HCB 0.03754189 0.17998819 0.17562234 -0.08375578
JPT 0.03604618 0.17562234 0.18375568 -0.08282565
YRI -0.08262898 -0.08375578 -0.08282565 0.05754685
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-0.007787 0.043225 0.092317 0.120507 0.166544 0.805405 1
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