[R] strangely long floating point with write.table()

[Berend Hasselman]

On 17-03-2014, at 21:03, Mike Miller <mbmiller+l at gmail.com> wrote:

> …...
> data[,c(5:9,11,13,17:21)] <- signif(data[,c(5:9,11,13,17:21)], digits=5)
> 
> Then write.table(data) does what I'd want.  It works better than format(). Example:
> 
>> data2 <- data
>> data2[,c(5:9,11,13,17:21)] <- signif(data2[,c(5:9,11,13,17:21)], digits=5)
>> 
>> write.table(format(data[1:10,], digits=5, trim=T), row.names=F, col.names=F, quote=F)
> 3100674 303164 6 1 -0.11869237 0.0073947 0.0084493 0.00012708 -0.1320 1 0 TT 1 GA 0 0 2 0.000 0 0.000 0.00000
> 3100765 303321 6 1 0.01434426 -0.0136545 -0.0017613 0.08502718 1.0365 1 1 CT 1 GA 1 0 1 0.000 0 1.000 1.00000
> 3101201 304352 6 1 -0.01710451 -0.0169568 0.0320392 0.00884896 0.4279 1 1 CT 2 GG 1 0 1 0.000 0 1.000 1.00000
> 3101862 305250 6 1 -0.01328316 0.0108479 -0.0170081 -0.03692398 -0.4470 1 0 TT 1 GA 0 0 2 0.000 1 1.000 1.00000
> 3103579 305847 6 1 0.01593935 0.0096043 -0.0437904 -0.02224669 -0.3365 1 0 TT 1 GA 0 0 2 0.000 0 0.000 0.00000
> 3103645 305961 6 1 0.20441289 -0.1090142 0.2727132 -0.29890268 1.5818 1 2 CC 0 AA 2 0 0 0.000 0 2.000 4.00000
> 3104098 308536 6 1 0.02842117 0.0562814 -0.0715448 -0.11510562 0.9974 1 0 TT 0 AA 0 1 1 0.944 0 0.944 0.89114
> 3104361 306928 6 1 -0.04840401 0.0266719 -0.0548747 -0.03640484 0.4499 1 0 TT 0 AA 0 0 2 0.000 1 1.000 1.00000
> 5100094 503136 6 1 0.19702704 -0.4104611 0.0869569 -0.03952420 0.3057 1 2 CC 0 AA 2 0 0 0.000 0 2.000 4.00000
> 5100938 503615 6 1 0.00098838 0.0267176 0.0451301 0.04790277 -0.1743 2 1 CT 0 AA 1 0 1 0.000 0 1.000 1.00000
>> 
>> write.table(data2[1:10,], row.names=F, col.names=F, quote=F)
> 3100674 303164 6 1 -0.11869 0.0073947 0.0084493 0.00012708 -0.132 1 0 TT 1 GA 0 0 2 0 0 0 0
> 3100765 303321 6 1 0.014344 -0.013654 -0.0017613 0.085027 1.0365 1 1 CT 1 GA 1 0 1 0 0 1 1
> 3101201 304352 6 1 -0.017105 -0.016957 0.032039 0.008849 0.4279 1 1 CT 2 GG 1 0 1 0 0 1 1
> 3101862 305250 6 1 -0.013283 0.010848 -0.017008 -0.036924 -0.447 1 0 TT 1 GA 0 0 2 0 1 1 1
> 3103579 305847 6 1 0.015939 0.0096043 -0.04379 -0.022247 -0.3365 1 0 TT 1 GA 0 0 2 0 0 0 0
> 3103645 305961 6 1 0.20441 -0.10901 0.27271 -0.2989 1.5818 1 2 CC 0 AA 2 0 0 0 0 2 4
> 3104098 308536 6 1 0.028421 0.056281 -0.071545 -0.11511 0.9974 1 0 TT 0 AA 0 1 1 0.944 0 0.944 0.89114
> 3104361 306928 6 1 -0.048404 0.026672 -0.054875 -0.036405 0.4499 1 0 TT 0 AA 0 0 2 0 1 1 1
> 5100094 503136 6 1 0.19703 -0.41046 0.086957 -0.039524 0.3057 1 2 CC 0 AA 2 0 0 0 0 2 4
> 5100938 503615 6 1 0.00098838 0.026718 0.04513 0.047903 -0.1743 2 1 CT 0 AA 1 0 1 0 0 1 1
> 
> format() with digits=5 is still showing 7 significant digits.  Why? signif() only shows 5.


From the help of format:

digits  "how many significant digits are to be used for numeric and complex x. The default, NULL, uses getOption("digits"). This is a suggestion: enough decimal places will be used so that the smallest (in magnitude) number has this many significant digits, and also to satisfy nsmall. (For the interpretation for complex numbers see signif.)”

So if I read this correctly the smallest number will have 5 significant digits. Larger numbers may get more. Given the fixed width (see argument trim).

Berend