Jørgen K. Kanters Jørgen K. Kanters - 3 months ago 12
R Question

How to write a special character in first line with write.table

I have a dataset

ped
which I want to write into a tab separated file. However the header needs to start with a hash (
#
) sign (due to the demands of the program who should read the file. How do I put the hash sign in there?

ped <- ped [,c('FAM_ID','IND_ID','FAT_ID','MOT_ID','SEX','DISEASE','RR','AGE')]
setwd(proj.dir)
write.table(ped, "DB/asymmetry.ped", sep="\t", row.names = FALSE, quote = FALSE)

Answer

You might try:

cat("#", file = "DB/asymmetry.ped")
write.table(ped, "DB/asymmetry.ped", sep="\t", row.names = FALSE, quote = FALSE,
            append = TRUE)

Note, you will get a warning message from write.table as this is the default behaviour:

## somewhere inside `write.table`:
if (!is.null(col.names)) {
        if (append) 
            warning("appending column names to file")

but it causes no harm.


Another possible way, is to append an "#" to your first column name, then use write.table as usual (with quote = FALSE):

ped <- ped [,c('FAM_ID','IND_ID','FAT_ID','MOT_ID','SEX','DISEASE','RR','AGE')]
NAMES <- names(ped)
NAMES[1] <- paste0("#", NAMES[1])
setwd(proj.dir)
write.table(ped, "DB/asymmetry.ped", sep="\t", row.names = FALSE, quote = FALSE,
            col.names = NAMES)

I would recommend this way. Let's have a test:

x <- trees[1:3, ]  ## use built-in dataset `trees`
NAMES <- names(x)
NAMES[1] <- paste0("#", NAMES[1])
## write to screen (stdout) for inspection
write.table(x, row.names = FALSE, col.names = NAMES, quote = FALSE)

#Girth Height Volume
8.3 70 10.3
8.6 65 10.3
8.8 63 10.2

In case you want to add an # at the start of every line / row, you can append a "#" column as the first column:

ped <- cbind.data.frame("#" = "#", ped[,c('FAM_ID','IND_ID','FAT_ID','MOT_ID','SEX','DISEASE','RR','AGE')])
setwd(proj.dir)
write.table(ped, "DB/asymmetry.ped", sep="\t", row.names = FALSE, quote = FALSE)

Again, let's have a test:

x <- cbind.data.frame("#" = "#", trees[1:3, ])
## write to screen (stdout) for inspection
write.table(x, row.names = FALSE, quote = FALSE)

# Girth Height Volume
# 8.3 70 10.3
# 8.6 65 10.3
# 8.8 63 10.2