I have filenames named <InputData>.<TestName>.csv and I'd like to make graphs for each test. The best way I can see to do this is to make one R table for each TestName. Each test produces the same columns of data, so I'd like to pull in all the data for each test into an R datatable with an extra column for the inputdata.
I'd like to do:
read.tables(c("B217.SE.csv", "C10.SE.csv"), sep=",")
produces (for example):
Filename col1 col2
1 B217.SE.csv 1 2
2 B217.SE.csv 2 4
3 C10.SE.csv 3 1
4 C10.SE.csv 4 5
What's the right way to do this? Some existing function I don't know about? Writing it out in the R language using a for loop?
I can't test it on your data, but you will want to use an apply type function like this:
data <- do.call("rbind", lapply(c("file1", "file2"), function(fn)
data.frame(Filename=fn, read.csv(fn)
))
Or, you can simplify it by using plyr. Here's a rough simulation of how that would work (using data frames instead of files):
> df1 <- data.frame(c1=1:5, c2=rnorm(5))
> df2 <- data.frame(c1=3:7, c2=rnorm(5))
In this case I will use get instead of read.csv:
> data <- ldply(c("df1", "df2"), function(dn) data.frame(Filename=dn, get(dn)))
> data
Filename c1 c2
1 df1 1 -0.15679732
2 df1 2 -0.19392102
3 df1 3 0.01369413
4 df1 4 -0.73942829
5 df1 5 -1.27522427
6 df2 3 -0.33944114
7 df2 4 -0.12509065
8 df2 5 0.11225053
9 df2 6 0.88460684
10 df2 7 -0.70710520
Edit
Taking Marek's suggestion, you can either overwrite or create your own function:
read.tables <- function(file.names, ...) {
require(plyr)
ldply(file.names, function(fn) data.frame(Filename=fn, read.csv(fn, ...)))
}
data <- read.tables(c("filename1.csv", "filename2.csv"))
Try this:
## take files.
files <- list.files(pattern=".csv")
## read data using loop
DF <- NULL
for (f in files) {
dat <- read.csv(f, header=T, sep="\t", na.strings="", colClasses="character")
DF <- rbind(DF, dat)
}
