r - Filter values in data frame

Question

Basically, I have a gene dataset in which the rows are genes and columns are sequential time points of protein folding. I need a function to filter genes of a certain threshold value from others across the entire data set, not just for certain vectors. For example:

          alpha98 alpha105 alpha112 alpha119
YAL002W      0.22     0.58    -0.36     0.13
YAL003W      0.05     0.55    -0.08     0.33

Any help would be great.

Answer 1

R is vectorized and R recycles. That means, that generally, something as simple as myDF > threshold will get you awfully close to what you need.

Specifically, it will give you a logical matrix of the same dimensions as your data.frame which will be TRUE when that cell in the DF exceeds the threshold (and FALSE otherwise).

You can then use that matrix as your tool to subset the data.frame.

myDF[myDF > threshold]