I have been running through the bioconductor introduction to ballgown and hit a snag in loading up the .ctab files using the method described therin.
The instructions suggest that if you store your data in a file structure like so:
Ballgowndata sample1_folder e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab sample2_folder e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab etc...
you should be able to load it using the dataDir function and a regular expression by which it matches your sample folders: Specifically it suggests creating a file Load.r
library(ballgown) data_directory = system.file('extdata', package='ballgown') bg = ballgown(dataDir=data_directory, samplePattern='sample', meas='all') save(bg, file='bg.rda')
and then using this script through the command line
R CMD BATCH load.R
I have done this very thing for the sample data provided with ballgown and it works, but when i try to use this method with my own data, which is stored in a folder with the following path
ballgown_inputs sample_SRR446038.bam e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab sample_SRR446039.bam e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab sample_SRR446040.bam e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab Etc...
It gives me an error output:
> library(ballgown) Attaching package: ‘ballgown’ The following object is masked from ‘package:base’: structure > data_directory = system.file('ballgown_inputs', package='ballgown') > bg = ballgown(dataDir=data_directory, samplePattern='sample', meas='all') Mon Mar 4 16:45:48 2019 Mon Mar 4 16:45:48 2019: Reading linking tables Error in file(file, "rt") : invalid 'description' argument Calls: ballgown -> read.table -> file Execution halted
From what little I've been able to find on the web this error seems to pretain to the inability to find the right path to the data. But I am unsure why that would be. It was my understanding that this dataDir function would search for the correct files, and it certainly worked with the toy dataset ballgown comes with. So why wont it work with mine?
Id greatly appreciate any light you could shed on this matter.