Cannot read file with “#” and space using read.table or read.csv in R

Question

I have a file where the first row is a header. The header can have spaces and the # symbol (there may be other special characters as well). I am trying to read this file usi

Answer 1

From the documentation (?read.csv):

comment.char character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.

The default is comment.char = "#" which is causing you trouble. Following the documentation, you should use comment.char = "".

Spaces in the header is another issue which, as mrdwab kindly pointed out, can be addressed by setting check.names = FALSE.

chromosomes <- read.csv(chromFile, sep = "\t", skip = 0, header = TRUE,
                        comment.char = "", check.names = FALSE)