Dear List members
I want to do the sliding window analysis of some specific values. Here is my
code:
require(zoo)
dat <- read.table("chr1.txt", header = TRUE, sep="\t")
dat2 <- cbind(dat[1,3]) #The first column is also important. It represents the
position of the site on the chromosome.
TS <- zoo(c(dat2))
a <- rollapply(TS, width=1000000, by=200000, FUN=mean, align="left") #The third
column values should roll against the first column values. I might be wrong
here with the code.
plot1 <- plot.default(a, col="red", type="l") #It returns me some errors for
this command.
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Part of the original data looks like as follows:
pos Fit Fst Fis
12794 0.928380160665041 -0.0877263098996843 0.934156378600823
12816 0.901040947621283 0.0382417096943425 0.897106109324759
12821 0.901040947621283 0.0382417096943425 0.897106109324759
12827 0.901040947621283 0.0382417096943425 0.897106109324759
12855 0.909446752933768 0.00347893012209298 0.909130624726955
13324 0.498125727088629 0.0975914515920549 0.443850267379679
13338 0.53827858671811 0.103194947279406 0.485148514851485
13339 -0.059306330783135 -0.0198369843236668 -0.038701622971286
13379 0.610641507226514 0.175889055559966 0.527541169789892
13381 0.144593428517224 -0.0343016958072985 0.172962226640159
13390 0.216526396327467 0.179801071155318 0.0447761194029849
13454 0.498125727088629 0.0975914515920549 0.443850267379679
13457 0.309860615307135 -0.0501399771889025 0.342812006319115
13462 0.536517915763086 -0.0302077737766018 0.550108147080029
That is, Fst against pos.
I am very willing to be educated concerning the mistakes I made for the code.
All the best
Li
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