Read column names with hyphen using read.table in R

Question

My column names have hyphens ("-"). When reading as table, the column names have (".") in place of ("-"). I want to retain the column names as-is.

df = read.table("meth_clin_kipan_pathanalysis.txt", header=T, sep="\t", row.names=1)

Raw:

TCGA-2K-A9WE-01A	TCGA-2Z-A9J1-01A
First	row
Second	row

Current output:

TCGA.2K.A9WE.01A	TCGA.2Z.A9J1.01A
First	row
Second	row

Desired output (same as raw, i.e., as-is):

TCGA-2K-A9WE-01A	TCGA-2Z-A9J1-01A
First	row
Second	row

Answer 1

Simply use check.names=FALSE argument of read.table to preserve original column names that have special characters and spaces.

Answer 2

This could work

library(dplyr)
df %>%
  rename_with(~stringr::str_replace_all(., '\\.', '-'), everything())