Ballgown data reading problem

Question

[Ricky]

Hi,

Problem: loading data into Ballgown returns error:

> bg = ballgown(dataDir = "ballgown", pData = pheno_data, samplePattern = "Col0")
Tue Jan 23 12:39:59 2018
Tue Jan 23 12:39:59 2018: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument

This is what I did. I am trying to load expression data from StringTie into Ballgown. The "ballgown" directory created by StringTie looks like so:

igz@igz-ubuntu-test ~/Priming/ballgown
$ ls
Col0C1  Col0C2  Col0C3  Col0T1  Col0T2  Col0T3  arabidopsis_phenodata.csv

with each sub dir containing the following files:

igz@igz-ubuntu-test ~/Priming/ballgown/Col0C1
$ ls
Col0C1.gtf  e2t.ctab  e_data.ctab  i2t.ctab  i_data.ctab  t_data.ctab

After starting an R session, I load packages (which already returns me a couple of errors):

 library(ballgown)

Attaching package: 'ballgown'

The following object is masked from 'package:base':

    structure

> library(RSkittleBrewer)
> library(genefilter)

Attaching package: 'genefilter'

The following object is masked from 'package:base':

    anyNA

> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:ballgown':

    contains, last

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(ggplot2)
> library(gplots)

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

> library(devtools)

I then set my working dir and load the pheno_data file:

> setwd("/home/igz/Priming/ballgown")
> getwd()
[1] "/home/igz/Priming/ballgown"
> pheno_data = read.csv("arabidopsis_phenodata.csv")
> pheno_data   
     ids treatment
1 Col0C1   control
2 Col0C2   control
3 Col0C3   control
4 Col0T1 triggered
5 Col0T2 triggered
6 Col0T3 triggered

Next I try to make a ballgown object, which seems to fail.

> bg = ballgown(dataDir = "ballgown", pData = pheno_data, samplePattern = "Col0")
Tue Jan 23 12:39:59 2018
Tue Jan 23 12:39:59 2018: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument

It seems that ballgown can't match data tables with the other arguments. when I check the "ballgown" dir for content I get the following:

> list.files("ballgown")
character(0)

Is it the problem that Ballgown doesn't find the data? How can I fix that?

Thanks, Ricky

[Ricky]

Fixed it! As Hugo suggested, the problem was to run Ballgown from the "ballgown" dir. Moved up one step, copied pheno_data csv to that dir and started session from there.

Thanks.

[Ricky]

Hello Ricky!

We believe that this post does not fit the main topic of this site.

solved

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[GenoMax]

closing a post is an action used by mods to flag duplicate/erroneous/incomplete posts. If a question has been solved then it should be marked accepted (green check mark) to provide closure to the thread.

I will move @hugo's comment to an answer which you should accept.

Answer 1

[Hugo]

Hi Ricky,

it seems that you are inside the "ballgown" directory and also telling that the directory that contains your data is "ballgown", which can be understood as "/home/igz/Priming/ballgown/ballgown". Give a try to: bg = ballgown(dataDir = "", pData = pheno_data, samplePattern = "Col0").

Regards,

Hugo.

[Ricky]

Thanks a lot,

tried it, but still the same problem.

> bg = ballgown(dataDir = "", pData = pheno_data, samplePattern = "Col0")
Tue Jan 23 14:30:30 2018
Tue Jan 23 14:30:30 2018: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument