Column names shift to left on read.table or read.csv - r

Question

Originally I have this TSV file (sample):
name type qty
cxfm 1C 0
d2 H50 2
g3g 1G 2
hb E37 1
nlx E45 4
so I am using read.csv to read data from a .tsv file but I always get this output:
name type qty
1 cxfm 1C 0
2 d2 H50 2
3 g3g 1G 2
4 hb E37 1
5 nlx E45 4
instead of getting this one:
name type qty
1 cxfm 1C 0
2 d2 H50 2
3 g3g 1G 2
4 hb E37 1
5 nlx E45 4
Any ideas this? this is what I am using to read the files:
file_list<-list.files()
for (file in file_list){
if (!exists("dataset")){
dataset <- read.table(file, header = TRUE, sep = "\t", row.names = NULL, blank.lines.skip = TRUE, fill = TRUE)
names(dataset) <- c("rowID", names(dataset)[1:ncol(dataset)-1])
}
if (exists("dataset")){
temp_dataset <- read.table(file, header = TRUE, sep = "\t", row.names = NULL, blank.lines.skip = TRUE, fill = TRUE)
names(temp_dataset) <- c("rowID", names(temp_dataset)[1:ncol(temp_dataset)-1])
dataset <- rbind(dataset, temp_dataset)
rm(temp_dataset)
}
}
dataset <- unique(dataset)
write.table(dataset, file = "dataset.tsv", sep = "\t")

Answer 1

There appears to be a missing column header in your source CSV file. One option here would be to leave your read.csv() call as it is and simply adjust the names of the resulting data frame:
df <- read.csv(file,
header = TRUE,
sep = "\t",
row.names = NULL,
blank.lines.skip = TRUE,
fill = TRUE,
comment.char = "",
quote = "", stringsAsFactors = FALSE)
names(df) <- c("rowID", names(df)[1:ncol(df)-1])

Answer 2

This is what I had to do to Fix it: set row.names to FALSE
write.table(dataset, file = "data.tsv", sep = "\t", row.names = FALSE)