Search
Question: Ballgown Error in file(file, "rt") : invalid 'description' argument
0
gravatar for vinayjrao
7 months ago by
vinayjrao0
vinayjrao0 wrote:

Hi, I am trying out the new tuxedo protocol (hisat, stringtie and ballgown). While calling the ballgown function with

bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data)

I get

Error in file(file, "rt") : invalid 'description' argument

Any help in this regard would be appreciated.

Thanks in advance :)

ADD COMMENTlink modified 7 months ago by Alyssa Frazee170 • written 7 months ago by vinayjrao0
0
gravatar for Alyssa Frazee
7 months ago by
Alyssa Frazee170
San Francisco, CA, USA
Alyssa Frazee170 wrote:

Hi there, this error usually means something went wrong with trying to read in the pData argument. The error comes from read.table, not from ballgown. More detail would be helpful in debugging here:

* what is "pheno_data" in your example? (is it a file path?)
* what are the contents of the file in that path?
* what happens when you try to read in whatever the pheno_data file is with read.table or read.csv? 

If you can get pheno_data file read in with a different function beforehand (read.table or read.csv), you can pass the resulting data frame directly to the ballgown function. But this error is coming from read.table, so if you solve that problem you will solve this one.

Hope that helps!

ADD COMMENTlink written 7 months ago by Alyssa Frazee170
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: 312 users visited in the last hour