Skip to content

Latest commit

 

History

History
77 lines (45 loc) · 3.69 KB

tab7_build_sequence_help.md

File metadata and controls

77 lines (45 loc) · 3.69 KB
Raw

Have any feedback? If you have any questions, comments, or suggestions, feel free to contact me at [email protected]

Requirements

This function handles .txt, .csv or .tsv file only

Your file must follow the N-columns (1 compound per line, N forms of he compound in column) format bellow prior to be loaded:

  • compound 1 ID, compound 1 form 1 mass, compound 1 form 2 mass, ...
  • compound 2 ID, compound 2 form 1 mass, compound 2 form 2 mass, ...

See the example file 4_generate_mass_pools_example_file.csv in the Demo folder.

Note that separator should be: comma, semicolon or tab

Algorithm

  • With the file containing 1 compound per line, create N (desired number of pools) pools by randomly dispatching lines in N dataframes.
  • For each dataframes, check that no mass are similar (including the mass tolerance parameter). If the dataframe pass the check, remove the lines from the input data, if not: delete the the dataframe.
  • Redo the previous step with N = N - number of pools that passed the check until N = 1
  • When N = 1, take the first line among the remaining lines from the input data, and try to add it to the first pool dataframe. Check if the resulting pool dataframe pass the check, if yes, keep the new pool and remove the line from the remaining lines in input data. If not, try to add the line to the second pool dataframe, etc.
  • Do it until the remaining lines from input data = 0.
  • If impossible, redo the process from the begining.

How optimal block size is determined?

If user check Automatic optimal block size button, the program tries to find the optimal sample block size considering the total number of samples.

From Min block size to Max block size it computes the all possible sample sequence blocks. Then it computes the variance of block sizes.

The optimal block size corresponds to one having the lower variance value.

Button functions

Load file box

Use the the Browse button to find your input file.

Always check the Header button because the input file must satisfy the header format described above.

Select Comma, Semicolon or Tab depending on the separator in your input file.

Mass to pool box

Displays the input table.

Use the show menu to inscrease the number of lines displayed in the view.

You can copy to clipboard or save the table using the Copy, CSV, Excel or PDF buttons.

Pool parameters box

Use the Number of pools numeric input to defined the desired number of final pools.

The Enter a mass tolerance text box allows to user to defined the mass tolerance to be considered for to compound to be in the same pool.

Maximum optimization iterations is a parameter setting the maximumn number of iterations for the calculation to find a set of pools all satisfying the mass tolerance parameter. If no pool can be find in the number of iteration. The function return a empty table.

The Maximum pooling iterations parameter is the maximum number of iterations for the algorithm to try adding all input lines in different pools. If some lines cannot be added to a pool, they are added to a final pool not satisfying the mass tolerance parameter.

Pooling information box

Displays 3 information on the relsuting pools:

  • The total number of pools
  • The pool size range
  • The ID of the smallest and the largest pools

Pool result box

The resulting pools are showed in this table.

Pool_index corresponds to the pool resulting pool IDs.

Use the show menu to inscrease the number of lines displayed in the view.

You can copy to clipboard or save the table using the Copy, CSV, Excel or PDF buttons.