将特定R包中的功能应用于文件夹中的所有文件

Question

I have a large table that I am reading into R as a data frame. After ordering and subsetting the df I break it into a list using the split() function. I then write that list out as individual text files. I am now reading the individual .txt files back into R so that I can determine the effectiveSize (from the coda package) of each file that does not lack Energy values. However I don't think this is the most efficient method. In any case, is there a way that I could apply the effectiveSize to each individual file or element of the list? When I test the effectiveSize function on one of the output files - effectiveSize(ASP29A[,3]) it works fine. But that's only one of 102 files/elements.

The original ordered data frame looks like this;

Chain  Res    Energy
 A    ALA28  -1.8046
 A    ALA28  -2.1910
 A    ALA28  -1.8403
 A    ALA28  -2.1813
 A    ALA28  -2.3693
 A    ALA28  -2.2808

I hope this is clear.

As a list, the data looks like

$ C.017500:'data.frame':    6003 obs. of  3 variables:
..$ Chain : Factor w/ 3 levels "A","B","C": 3 3 3 3 3 3 3 3 3 3 ...
..$ Res   : chr [1:6003] "017500" "017500" "017500" "017500" ...
..$ Energy: num [1:6003] -37 -33.8 -34.7 -35.4 -35 ...

$ A.ALA28 :'data.frame':    6003 obs. of  3 variables:
..$ Chain : Factor w/ 3 levels "A","B","C": 1 1 1 1 1 1 1 1 1 1 ...
..$ Res   : chr [1:6003] "ALA28" "ALA28" "ALA28" "ALA28" ...
..$ Energy: num [1:6003] -1.8 -2.19 -1.84 -2.37 -2.18 ...

And so on through 102 elements.

Answer 1

Here's how I would do it:

• Read the file list using:

   setwd("path/to/files/") file.list <- dir(pattern = "txt$") 

  The pattern bit is optional, but it can help you filtering only some files.

• Use sapply to run whatever function you want

   res <- sapply(file.list, yourfunction) 

For instance, to know the file size of the files you could use:

res <- sapply(file.list, file.size)

You may want to create function to call effectiveSize , such as:

eff.size <- function(filename)
      {
      data <- read.table(filename)
      # <do something here with the data as needed>
      res <- effectiveSize(<appropriate parameters>)

      # return the result
      res
      } 

Then call

 res <- sapply(file.list, eff.size)