| pop1 | pop2 | est | se |
|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> |
| AA | Ami | 0.04942118 | 0.0003878861 |
| AA | Atayal | 0.05464286 | 0.0004206249 |
| AA | Basque | 0.03370974 | 0.0003165638 |
| AA | BedouinB | 0.03139797 | 0.0003027369 |
| AA | Biaka | 0.01256080 | 0.0001514436 |
| ⋮ | ⋮ | ⋮ | ⋮ |
| Surui | Ulchi | 0.04615105 | 0.0005242951 |
| Surui | Yoruba | 0.08793567 | 0.0005744330 |
| Tubalar | Ulchi | 0.01139411 | 0.0001463168 |
| Tubalar | Yoruba | 0.04703516 | 0.0003102144 |
| Ulchi | Yoruba | 0.05555142 | 0.0003697745 |
| pop1 | pop2 | pop3 | est | se | z | p |
|---|---|---|---|---|---|---|
| <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> |
| AA | Yoruba | Basque | -0.004777214 | 0.0001110123 | -43.03319 | 0 |
| AA | Yoruba | Sardinian | -0.004585963 | 0.0001110581 | -41.29336 | 0 |
| AA | Yoruba | Georgian | -0.004319089 | 0.0001057450 | -40.84436 | 0 |
| AA | Yoruba | Kalash | -0.004086874 | 0.0001085978 | -37.63311 | 0 |
| AA | Yoruba | Brahui | -0.003913767 | 0.0000985930 | -39.69619 | 0 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AA | Yoruba | Mbuti | 0.002164048 | 8.005551e-05 | 27.03184 | 6.245131e-161 |
| AA | Yoruba | Biaka | 0.002384887 | 7.849669e-05 | 30.38201 | 9.494679e-203 |
| AA | Yoruba | Mandenka | 0.002521384 | 7.111747e-05 | 35.45380 | 2.534922e-275 |
| AA | Yoruba | Yoruba | 0.003055913 | 7.271039e-05 | 42.02856 | 0.000000e+00 |
| AA | Yoruba | Esan | 0.003063343 | 7.891989e-05 | 38.81585 | 0.000000e+00 |
- 'Altai_Neanderthal.DG'
- 'Denisova.DG'
- 'French'
- 'Han'
- 'Mbuti'
- 'Papuan'
- 'Primate_Chimp'
- 'Vindija_Neanderthal.DG'
- 'Yoruba'
![\"F4-ratio\"](\"F4.large.jpg\")
\n",
" \n",
" and estimate the admixture proportion $\\alpha$ as\n",
" $$\\alpha = \\frac{f_4(A, O; X, C)}{f_4(A, O; B, C)}$$\n",
" \n",
"\n",
"**Task 3**: Use the `qpf4ratio`-function in `admixtools` to use the ancient data (that we used for the $D$-stats exercise to estimate the Neandertal ancestry in French, Han and Papuans.\n",
"\n",
"- have a look at `?qpf4ratio` to figure out the arguments this function expects\n",
"- which population is in which position of the arguments? Construct a vector `v` or data frame that matches this order\n",
"- run the f4-ratio-estimation using `qpf4ratio(ancient, v)\n",
"- do the archaic ancestries differ between the three populations?"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"| qpf4ratio {admixtools} | R Documentation |
Estimate admixture proportions via f4 ratios
\n", "\n", "Description
\n", "\n", "Estimate admixture proportions via f4 ratios\n", "
\n", "\n", "\n", "Usage
\n", "\n", "\n",
"qpf4ratio(data, pops, boot = FALSE, verbose = FALSE)\n",
"\n",
"\n",
"\n",
"Arguments
\n", "\n", "data | \n",
"\n",
" Input data in one of three forms:\n", " \n", "\n", "
|
pops | \n",
"\n",
" A vector of 5 populations or a five column population matrix.\n",
"The following ratios will be computed: |
boot | \n",
"\n",
" If |
verbose | \n",
"\n",
" Print progress updates \n", " |
Value
\n", "\n", "qpf4ratio returns a data frame with f4 ratios\n",
"
[Package admixtools version 2.0.0 ]
"
],
"text/latex": [
"\\inputencoding{utf8}\n",
"\\HeaderA{qpf4ratio}{Estimate admixture proportions via f4 ratios}{qpf4ratio}\n",
"%\n",
"\\begin{Description}\\relax\n",
"Estimate admixture proportions via f4 ratios\n",
"\\end{Description}\n",
"%\n",
"\\begin{Usage}\n",
"\\begin{verbatim}\n",
"qpf4ratio(data, pops, boot = FALSE, verbose = FALSE)\n",
"\\end{verbatim}\n",
"\\end{Usage}\n",
"%\n",
"\\begin{Arguments}\n",
"\\begin{ldescription}\n",
"\\item[\\code{data}] Input data in one of three forms:\n",
"\\begin{enumerate}\n",
"\n",
"\\item{} A 3d array of blocked f2 statistics, output of \\code{\\LinkA{f2\\_from\\_precomp}{f2.Rul.from.Rul.precomp}} or \\code{\\LinkA{f2\\_from\\_geno}{f2.Rul.from.Rul.geno}} (fastest option)\n",
"\\item{} A directory which contains pre-computed f2-statistics\n",
"\\item{} The prefix of genotype files (slowest option)\n",
"\n",
"\\end{enumerate}\n",
"\n",
"\n",
"\\item[\\code{pops}] A vector of 5 populations or a five column population matrix.\n",
"The following ratios will be computed: \\AsIs{f4(1, 2; 3, 4)/f4(1, 2; 5, 4)}\n",
"\n",
"\\item[\\code{boot}] If \\code{FALSE} (the default), block-jackknife resampling will be used to compute standard errors.\n",
"Otherwise, block-bootstrap resampling will be used to compute standard errors. If \\code{boot} is an integer, that number\n",
"will specify the number of bootstrap resamplings. If \\code{boot = TRUE}, the number of bootstrap resamplings will be\n",
"equal to the number of SNP blocks.\n",
"\n",
"\\item[\\code{verbose}] Print progress updates\n",
"\\end{ldescription}\n",
"\\end{Arguments}\n",
"%\n",
"\\begin{Value}\n",
"\\code{qpf4ratio} returns a data frame with f4 ratios\n",
"\\end{Value}"
],
"text/plain": [
"qpf4ratio package:admixtools R Documentation\n",
"\n",
"_\bE_\bs_\bt_\bi_\bm_\ba_\bt_\be _\ba_\bd_\bm_\bi_\bx_\bt_\bu_\br_\be _\bp_\br_\bo_\bp_\bo_\br_\bt_\bi_\bo_\bn_\bs _\bv_\bi_\ba _\bf_\b4 _\br_\ba_\bt_\bi_\bo_\bs\n",
"\n",
"_\bD_\be_\bs_\bc_\br_\bi_\bp_\bt_\bi_\bo_\bn:\n",
"\n",
" Estimate admixture proportions via f4 ratios\n",
"\n",
"_\bU_\bs_\ba_\bg_\be:\n",
"\n",
" qpf4ratio(data, pops, boot = FALSE, verbose = FALSE)\n",
" \n",
"_\bA_\br_\bg_\bu_\bm_\be_\bn_\bt_\bs:\n",
"\n",
" data: Input data in one of three forms:\n",
"\n",
" 1. A 3d array of blocked f2 statistics, output of\n",
" ‘f2_from_precomp’ or ‘f2_from_geno’ (fastest option)\n",
"\n",
" 2. A directory which contains pre-computed f2-statistics\n",
"\n",
" 3. The prefix of genotype files (slowest option)\n",
"\n",
" pops: A vector of 5 populations or a five column population matrix.\n",
" The following ratios will be computed: f4(1, 2; 3, 4)/f4(1,\n",
" 2; 5, 4)\n",
"\n",
" boot: If ‘FALSE’ (the default), block-jackknife resampling will be\n",
" used to compute standard errors. Otherwise, block-bootstrap\n",
" resampling will be used to compute standard errors. If ‘boot’\n",
" is an integer, that number will specify the number of\n",
" bootstrap resamplings. If ‘boot = TRUE’, the number of\n",
" bootstrap resamplings will be equal to the number of SNP\n",
" blocks.\n",
"\n",
" verbose: Print progress updates\n",
"\n",
"_\bV_\ba_\bl_\bu_\be:\n",
"\n",
" ‘qpf4ratio’ returns a data frame with f4 ratios\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"?qpf4ratio"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"pop_mat = expand.grid('Altai_Neanderthal.DG', 'Primate_Chimp', c('French', 'Papuan', 'Han'), c('Yoruba'), 'Vindija_Neanderthal.DG' ) %>% as.matrix"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/html": [
"| pop1 | pop2 | pop3 | pop4 | pop5 | alpha | se | z |
|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> |
| Altai_Neanderthal.DG | Primate_Chimp | French | Yoruba | Vindija_Neanderthal.DG | 0.02067599 | 0.002513743 | 8.225182 |
| Altai_Neanderthal.DG | Primate_Chimp | Papuan | Yoruba | Vindija_Neanderthal.DG | 0.03070703 | 0.003833748 | 8.009663 |
| Altai_Neanderthal.DG | Primate_Chimp | Han | Yoruba | Vindija_Neanderthal.DG | 0.02205858 | 0.002959204 | 7.454227 |