run mist through main.R

[m116]

I am getting stared with MiST for analysis PPI with discrete data (spectral counts and unique counts). Unfortunately, when I run "./main.R", error occurred, Please help!!! Thank you very much!

Loading required package: geepack
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-2

Attaching package: ‘MESS’

The following object is masked from ‘package:glmnet’:

auc

[1] "!!! Error loading the config file. Please make sure the file follows YAML format."
Error in value[3L] : no loop for break/next, jumping to top level
Calls: main ... tryCatch -> tryCatchList -> tryCatchOne ->
Execution halted

[jvondollen]

This sounds like there might be a character in the YAML file that is out of place. Sometimes a blank space will upset things, so check to make sure there are not any trailing white spaces after any of the lines. Could you share the contents of the yaml file?

[jvondollen]

Also make sure you have installed package "yaml".

[jvondollen]

Another possibility is that the file paths are not from the root directory. Please make sure the full path (from the root directory) is given for any files referenced in the YAML config file.

[jvondollen]

There are some new updates to the repository to help with the specificity of the error handling. Please update your files and let me know if the problem persists.

[m116]

Hi jvondollen,

Thank you very much. I have got a protocol. I will try according the protocol.

Best!

cheney

[hemingwang]

Hi,
When I run the example, I meet this wrong:
My code is :
Rscript main.R -c tests/small/mist_small_test.yml
My result :

LOADING DEPENDENCIES...
All required R libraries accounted for.
PREPROCESSING FILES
READING FILES
!! DUPLICATE ID/PREY PAIRS FOUND IN DATA! DUPLICATES REMOVED
FILTERING COMMON CONTAMINANTS
FILTERED 116 CONTAMINANTS
MERGING KEYS WITH DATA
12 TOTAL BAITS DETECTED
12/12 BAITS DETECTED IN DATA FILE
12/12 BAITS DETECTED IN KEYS FILE
CONVERTING TO MATRIX
DIFFERENT MOLECULAR WEIGHTS DETECTED FOR THE FOLLOWING PREY:
P05141
P25398
P50914
Q00839
Q6PEY2
Q96EY1
Q9ULX6
P14866
P23588
Q8IWX8
P07814
Q00341
Q04637
O95163
O95757
P09651
P30837
P41252
Q14444
Q9ULT8
O75369
P53621
Q96HC4
Q9H4A3
USING MEDIAN WEIGHT PER PROTEIN
QUALITY CONTROL
Saving 7 x 7 in image
Error: StatBin requires a continuous x variable: the x variable is discrete.Perhaps you want stat="count"?
Backtrace:
█

1. └─global::main(opt)
2. └─global::qc.main(...)

3. └─global::qc.ipDists(data_matrix, ip_baits, matrix_file)
   

4.   └─ggplot2::ggsave(...)
   

5.     ├─grid::grid.draw(plot)
   

6.     └─ggplot2:::grid.draw.ggplot(plot)
   

7.       ├─base::print(x)
   

8.       └─ggplot2:::print.ggplot(x)
   

9.         ├─ggplot2::ggplot_build(x)
   

10.         └─ggplot2:::ggplot_build.ggplot(x)
    

11.           └─ggplot2:::by_layer(function(l, d) l$compute_statistic(d, layout))
    

12.             └─ggplot2:::f(l = layers[[i]], d = data[[i]])
    

13.               └─l$compute_statistic(d, layout)
    

14.                 └─ggplot2:::f(..., self = self)
    

15.                   └─self$stat$setup_params(data, self$stat_params)
    

16.                     └─ggplot2:::f(...)
    

Execution halted