R：read.table在调用列时检测制表符分隔的文件中缺少值的问题

Question

I am trying to do something very simple and am having a heck of a time with it. I have a set of data that is stored in a tab-delimited file. In this tab-delimited file, there are missing values. When I try to call the column that has the tab-separated values, the wrong column is called. I believe this is because the first value after the header line in the third column (the one I am trying to extract) is a column with a missing vlaue. Here is an example of my data (my actual data is 36000 lines, but all formatted the same):

x   y   z   
230.125 49.875  0
230.375 49.875  0
230.625 49.875  0
261.125 49.875  0
261.375 49.875  0
251.625 48.875  4.38619211912155
251.875 48.875  3.70883572995663
252.125 48.875  3.2566264629364
252.375 48.875  3.00820730924606
254.125 48.875  7.88962166309357
254.375 48.875  8.50787222385406
254.625 48.875  8.95758244991303
254.875 48.875  9.47213044166565
255.125 48.875  9.96883320808411
255.375 48.875  10.4400730609894
255.625 48.875  10.6357674837112
255.875 48.875  9.81607600450516
274.125 48.875  0
274.375 48.875  0
274.625 48.875  0
274.875 48.875  0
275.125 48.875  0
275.375 48.875  0
275.625 48.875  0
275.875 48.875  0
276.125 48.875  0

I am trying to extract the third column and append it to another matrix to do calculations with later (this will be done for many files of the same type). That's why I have a second matrix initialized here.

Here is my code:

library(data.table)
temp <- c()
matrix_prelim <- matrix(nrow = 36000)
temp <- as.matrix(read.table("/myfilepath/example.txt", sep="\t", fill = TRUE. na.strings = "", header=TRUE)
matrix_prelim <- cbind(matrix_prelim, temp[[3]])

Then printing:

head(matrix_prelim)

yields:

      [,1]    [,2]
[1,]    NA 230.625
[2,]    NA 230.625
[3,]    NA 230.625
[4,]    NA 230.625
[5,]    NA 230.625
[6,]    NA 230.625

when what I would like is (knowing that initializing the matrix with no contents will give me a column of NAs, which is no problem):

      [,1]             [,2]
[1,]    NA                0
[2,]    NA                0
[3,]    NA                0
[4,]    NA                0
[5,]    NA                0
[6,]    NA 4.38619211912155

I have absolutely no idea what I am doing wrong. Any help would be much appreciated.

Thank you!

EDIT: I should note that I have tried changing the na.strings argument to " ", taking the na.strings argument out completely, tried using fread and grabbing the third column (that just simply didn't work at all), and tried setting headers = FALSE.

Answer 1

Though you have called library(data.table) , you're not actually converting your data to data.table format. Instead you're data is likely read in as a data.frame , which is fine.

There is no need to initialize a matrix to store your 3rd column as a separate vector. Try something like this:

temp <- as.matrix(read.table("/myfilepath/example.txt", sep="\t", fill = TRUE. na.strings = "", header=TRUE)
matrix_prelim <- temp[3]

Let me know if this works.