How to combine different .csv files to one complete file by adding the data of every file as an additional row using R?

问题

I have several different folders which all contain one single .csv file. All of those .csv files have one single column containing the data of one condition of an experiment. I would like to merge those .csv files in such a way that the data of every file is added as a new column.

At the moment, it Looks somehow like this:

However, it would like to have one single .csv file, where all the separate files are copied into a new column containing the name of the source file, like:

C1     C2     ...    Cn
102    296    ...    ...
106    299    ...
152    843    ...
196    1033   ...
223    1996   ...
486           ...
553           ...

So far, I the following code:

myFiles = list.files(path = ".", recursive = TRUE, pattern = ".csv", full.names = TRUE)
data <- lapply(myFiles, read.table, sep="\t", header=FALSE)
Max <- max(sapply(data, length))
data <- lapply(data, function(x) c(x, rep(NA, Max - length(x))))
data <- do.call(cbind, data)
names(data) <- sub("^[^[:alnum:]]*([[:alnum:]]+)\\.csv$", "\\1", myFiles)

write.csv(data, "outfile.csv")

It yielded a document that looks like this instead of adding the data of every .csv file in a new column:

enter image description here

回答1:

One can read all files using read.table in a list. Combine all data using dplyr::bind_rows. Afterwards, use reshape2::dcast to spread data in wide format with a column for data from every file.

# Get list of files in directory
fileList <- list.files(".", "*.csv", full.names = TRUE)

# Read file data. This will generate a list containing dataframes
listData <- lapply(fileList, read.table)

# Name list using name of files
names(listData) <- gsub(".csv","",basename(fileList))

library(tidyverse)
library(reshape2)

bind_rows(listData, .id = "FileName") %>%
  group_by(FileName) %>%
  mutate(rowNum = row_number()) %>%
  dcast(rowNum~FileName, value.var = "V1") %>%
  select(-rowNum) %>%
  write.csv(file="Result.csv")

# Content of Result.csv
# "","C1","C2"
# "1",102,296
# "2",106,299
# "3",152,843
# "4",196,1033
# "5",223,1996
# "6",486,NA
# "7",553,NA

回答2:

Is this what you want?
Note that I read the files in with scan. Since the files have only one column there is no need for a complex function like read.csv.

myFiles <- list.files(path = ".", pattern = "^C.*\\.csv", full.names = TRUE, recursive = TRUE)
data <- lapply(myFiles, scan)
Max <- max(sapply(data, length))
data <- lapply(data, function(x) c(x, rep(NA, Max - length(x))))
data <- do.call(cbind, data)
names(data) <- sub("^[^[:alnum:]]*([[:alnum:]]+)\\.csv$", "\\1", myFiles)

write.csv(data, "outfile.csv")

The contents of "outfile.csv" are

"","V1","V2"
"1",102,296
"2",106,299
"3",152,843
"4",196,1033
"5",223,1996
"6",486,NA
"7",553,NA

来源：https://stackoverflow.com/questions/50897193/how-to-combine-different-csv-files-to-one-complete-file-by-adding-the-data-of-e

标签

csv

merge

row