9.15 Reading in PBS data

We’ve pre-calculated pairwise \(\textrm{F}_{ST}\) between the Rampasasa, Han Chinese, and Papua New Guinea populations. Load the results for chromosome 11 into R:

fst_results <- read.table("fst_results.txt.gz", header = TRUE)
head(fst_results)

##   chr       pos    rps.af    chb.af    png.af fst.rps.chb fst.rps.png
## 1  11 100001950 0.1666670 0.0145631 0.0428571  0.32524800   0.0845486
## 2  11 100003476 0.0555556 0.0339806 0.1000000 -0.01078610  -0.0118052
## 3  11 100004351 0.1111110 0.0485437 0.1142860  0.05945300  -0.0322152
## 4  11 100005864 0.6111110 0.6553400 0.4285710 -0.02752900   0.0520164
## 5  11 100006486 0.8333330 0.7766990 0.7571430  0.00768713  -0.0119055
## 6  11 100006861 0.5000000 0.3834950 0.2285710  0.05413630   0.1807550
##   fst.png.chb
## 1  0.00465910
## 2  0.03640770
## 3  0.02896550
## 4  0.11842600
## 5 -0.00951234
## 6  0.06338550

Every row of this table is a SNP:

Columns ending in .af contain the allele frequency for that population
Columns starting with fst. contain the \(\textrm{F}_{ST}\) between that population pair