Error in reading tab delimited file

Question

[arshad1292]

I have two files 1) leafdata file with readcount values 2) metadata file with sample information... both are in tab delimited format. They look like this:

Data file:

genus                     sample1 sample2 sample3 sample4 ........ sample206
Massilistercora           26       419    16      2974             159
Aminipila                 104      59     183     2594             209
Mogibacterium             502      971    591     218              2974 
Flintibacter              418      0      981     2397             264
.
.

Metadata file:

samplename    group      timepoint   gender
sample1       case       A           M
sample2       control    B           F
sample3       control    A           F
.
.
.
sample206     case       E           M

I loaded the data into R as below:

testdata <- read.table("leafdata.txt", sep = "\t", header = TRUE, check.names = FALSE)

Then checked the dimension as below:

dim(testdata)
2874 207

However when I loaded the metadata as below:

leafmetadata <- read.table("metadata.txt", sep = "\t", header = TRUE, check.names = FALSE)

Then dimensions as below:

dim(leafmetadata)
206 4 

My question is why do I get number 206 for metadata but 207 for the leafdata even though my sample number is same in both files? This is what causing error for further analysis. Am I reading the file incorrectly in R?

I would really appreciate if some expert could please help me to solve this issue. Many thanks in advance!

[cpad0112]

There is no error and please go through your data before you post this kind of queries. Hint: "genus"

[arshad1292]

Thanks for pointing that out. I also tried by removing "genus" but still get the same error.

[Kevin Blighe]

You need dos2unix or unix2dos, depending on which system you are using, and the system on which the file was created.

[cpad0112]

Can you try following code in R (one or both of them) and print the output here?:

> length(names(testdata)[!names(testdata) %in% "genus"])    
> isTRUE(all.equal (leaftmetadata$samplename, names(testdata)[!names(testdata) %in% "genus"]))
> identical (leaftmetadata$samplename, names(testdata)[!names(testdata) %in% "genus"])

Assuming that following data exists:

testdata <- read.table("leafdata.txt", sep = "\t", header = TRUE, check.names = FALSE)
leafmetadata <- read.table("metadata.txt", sep = "\t", header = TRUE, check.names = FALSE)
length(names(testdata)[!names(testdata) %in% "genus"])