Reading in a matrix to R

Question

I have a matrix in a file in the following format:

         V1        V2        V3        V4        V5       V6        V7
[1,] 17.67787 12.375978 12.007860 16.089949 24.864464 37.64243 42.711561
 ...
[10,] 42.89655 21.535867  7.975470  6.580414 10.326551 11.06297 11.201733
        V8       V9      V10       V11       V12       V13       V14
[1,] 30.41993 35.46864 16.97427 10.992030 11.408483 17.417670 33.815149
 ...
[10,]

10 rows and N column vectors laid out in sets of 7 columns.

How would one go about reading this into R as a matrix?

scan is throwing an error:

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  scan() expected 'a real', got 'V1'

If I try to call "as.matrix(read.table(..))"

I get:

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 11 did not have 8 elements

I think it would be helpful to post an actual head -11 of the file in question. Having said that, if additional column headers (like V9- V16) are really interspersed within the file, then you'll need to use readLines, roll up your sleeves and do some post-processing. — hrbrmstr
Editing my post to include an actual extract of the files I need to read in. — tanbog
@akun I get: Error in read.table("centroid0.txt", fill = TRUE, header = TRUE) : duplicate 'row.names' are not allowed — tanbog
@raf please check my solution below. I just copied the data from pastebin and run it using readLines(textConnection( or you can just read it from file by readLines("name.txt") — akrun

akrun akrun · Accepted Answer · 2014-10-05T07:03:25

You could try:

 lines <- readLines(textConnection("V1 .... #... all the data you showed in `pastebin`
                 ...   33.21421"))

If you are reading it from a file

 lines <- readLines("raf.txt")
 lines1 <- gsub("\\[.*]","",lines) #remove the `[,number]` part in the beginning
 library(stringr)
 lines2 <- str_trim(lines1) #remove the trailing/leading spaces

Here, I am splitting the lines2 into groups in a list using an index created by grep and cumsum so that each set of new group has a header and the data. Then read the files in the list using lapply and read.table

  lst1 <- lapply(split(lines2, cumsum(grepl("^V", lines2))), 
                  function(x) read.table(text=x, header=TRUE))
  names(lst1) <- NULL
  res <- do.call(`cbind`, lst1)

If you want to convert it to matrix

 m1 <- as.matrix(res)
 dim(res)
 #[1]  10 128

 res[1:3,1:3]
 #       V1       V2       V3
 #1 17.67787 12.37598 12.00786
 #2 29.44688 19.44888 15.06014
 #3 30.49377 19.64495 11.15946

Reading in a matrix to R

2 Answers