README for dataRetainer.

Release v1.0
May 2021
Sharlee Climer


'dataRetainer' is a program for cleaning data to remove rows/columns with  
excessive missing values. On each iteration, the user selects the 
maximum percent missing for rows and columns, then the percent
missing is updated after removing the rows and columns are removed.

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The usage can be found by typing './dataRetainer' on the command line.  
It follows:

Fatal: Usage:

   dataRetainer input.txt numDataRows numDataColumns numHeaderRows numHeaderCols

where 

- 'input.txt' is your data file

- 'numDataRows' is the number of data rows, without counting headers

- 'numDataColumns' is the number of data columns, without counting headers

- 'numHeadRows' is the number of header rows in 'input.txt'

- 'numHeadCols' is the number of header columns in 'input.txt'

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*** Important note about input file: ***

- Each string in the header rows and/or columns must be continuous
  with no internal white space.
  
- Treated as missing values if start with: N, ?, X

- A custom missing symbol can be defined in 'miss.h'

- Program can be used for genotype data with a space between alleles
  by setting 'SNP_DATA' to 1 in 'miss.h'. (Note that '-' will be treated
  as missing data when in this mode.)

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Output will be written to a file with the same name as 'input.txt', but
with the last four characters replaced with 'cleaned.tsv'. This is a
plain text file with values separated by tabs.

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If LOG_FILE is set to 1 in 'dataRetainer.h' (default), a log file with the same name 
as the input file (minus the last four characters plus '.miss.log') will
record the choices of each iteration and record the rows and columns removed, 
relative to the current revision. If the same input file is run more
than once, the output will be appended to the logfile.

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A small teat file is included and can be run by typing the following:

./dataRetainer small_gex.txt 10 10 1 1

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Contact climer@umsl.edu with questions, bug reports, etc.