Merging more than 2 csv files in R

Question

[oqp5041]

Hello!

How do I merge more than two csv files in R based on gene_id and log2.fold_change? Is there a easy code or package for it? Thank you.

[Rob]

I believe the standard way to do this is by successively merging into a resulting dataframe. That is, if you wish to merge e.g. [1,2,3,4,5], you'd do merge(1, merge(2, merge(3, merge(4, 5) ) ) ). This is actually supported explicitly in Pandas — one place where I wish R's dataframes had the same built-in capabilities.

[zx8754]

See relevant SO post:

• Simultaneously merge multiple data.frames in a list

Answer 1

[Devon Ryan]

The fastest way to do this is with the dplyr package. This follows the same procedure as Rob mentioned in his comment above, but using dplyr::inner_join() is much faster.

Answer 2

[Ram]

Adding an updated answer for completeness' sake

The way I do this is using lapply and Reduce

dat.files <- list.files("*.csv") #whatever you need to get the files listed
dat <- lapply(dat.files, read.table, sep=",", ...)
## Now process dat so column names are consistent etc. - you might need a loop
## Once done,

dat <- Reduce(merge, dat) # or Reduce(dplyr::inner_join, dat)