Search
Tutorial: Importing multiple .h5 files using tximport
0
gravatar for nelson.s.garcia
9 weeks ago by
nelson.s.garcia0 wrote:

I am having trouble with importing kallisto files for DESeq analysis in R. I went to the tutorial website and found this: 

files <- file.path(dir, "kallisto_boot", samples$run, "abundance.h5")
names(files) <- paste0("sample", 1:6)
txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE)
head(txi.kallisto$counts)

I have fifteen .h5 files to import in total. I can't quite figure out how to do it with the R script above. 

Is "kallisto_boot" something that I need to make prior to importing the files? 

What does samples$run do?

Should I replace "abundance.h5" with the fifteen .h5 files that I need to import?

Thank you very much.

ADD COMMENTlink modified 9 weeks ago by Steve Lianoglou12k • written 9 weeks ago by nelson.s.garcia0

Thanks. How can I create the vector?

ADD REPLYlink written 9 weeks ago by nelson.s.garcia0

It's a character vector that lists the files.

First you need to locate the files on your laptop or cluster and make sure that you point to them correctly (either using relative or absolute paths).

files <- c("/path/to/file1.h5", "/path/to/file2.h5")
ADD REPLYlink written 9 weeks ago by Michael Love18k
0
gravatar for Michael Love
9 weeks ago by
Michael Love18k
United States
Michael Love18k wrote:

That’s just demo code which points to the demo files. All you need to do is have files point to your h5 files, however you want to create that vector.

ADD COMMENTlink written 9 weeks ago by Michael Love18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 226 users visited in the last hour